A wizard who casts the 8th-level Sor/Wiz spell polymorph any object [trans] (Player's Handbook 263) so as to change a rock into a troll (Monster Manual 247–8) doesn't change that rock into a troll that possesses the extraordinary ability regeneration because the subject of the 4th-level Sor/Wiz spell polymorph [trans] (PH 263) "does not gain the extraordinary special qualities possessed by the new form."
Likewise, a wizard who casts the polymorph any object spell on a rock can't change that rock into a dread wraith (MM 257–8) because from the polymorph spell the polymorph any object spell inherited all of that it can't result in a creature possesses the undead type and that it "can’t cause a subject… to assume an incorporeal… form," and that "the assumed form [has] a maximum of 15 H[it] D[ice]…." (A dread wraith has 16 HD.)
The polymorph any object spell doesn't remove the polymorph spell's restrictions by saying that "it changes one object or creature into another" then not offering details. Those details aren't offered because those details are included with the polymorph spell, which the polymorph any object spell functions as except in the ways that the polymorph any object spell itself does detail.
Getting from there to here
The 2nd-level Sor/Wiz spell alter self [trans] (Player's Handbook 197), in part, says, "You assume the form of a creature of the same type as your normal form."
The 4th-level Sor/Wiz spell polymorph [trans] (PH 263), in part, says, "This spell functions like alter self, except that you change the willing subject into another form of living creature." Hence, instead of only being able to affect the caster like the alter self spell, the polymorph spell can affect any willing subject. (The spell's header material also makes it so that the subject must be living—most constructs, deathless, and undead can't be affected by a polymorph spell.)
The 8th-level Sor/Wiz spell polymorph any object [trans] (PH 263), in part, says, "This spell functions like polymorph, except that it changes one object or creature into another." Hence, instead of only being able to affect willing and living creatures like the polymorph spell, the polymorph any object spell can affect any creature or object. (The spell's header material also makes it so that an object must be nonmagical and no more than 100 cu. ft. per level. Because it's an effect mandating a Fortitude saving throw that also affects objects, constructs, deathless, and undead can be affected by the polymorph any object spell.)
The polymorph any object spell is still like the polymorph spell except where it says that it is not, and where it is not like the polymorph spell is detailed immediately after it says, "This spell functions like polymorph, except that it changes one object or creature into another."
That is, the polymorph any object then goes on to explain that the spell's duration is not the polymorph spell's 1 min/level but, instead, determined arbitrarily by the DM. (To what kingdom does a fire elemental belong?) Also, "[u]nlike polymorph, polymorph any object does grant the creature the Intelligence score of its new form." Further, because the polymorph any object spell can, essentially, create life, it adds, "If the original form didn’t have a Wisdom or Charisma score, it gains those scores as appropriate for the new form." Finally, it goes on for a few paragraphs about how the spell interacts with objects (because the polymorph spell doesn't interact with objects at all). And, by the way, it says that a caster can employ a polymorph any object spell so that it duplicates a handful of other spells. And, in case you missed it, the header material gives the polymorph any object spell a range of close. (The polymorph spell's range is touch.)
These are the extent of the polymorph any object spell's differences from the polymorph spell. The polymorph any object spell makes no other modifications to the polymorph spell's rules, like what is gained or lost when the new form is a creature.
Saying that Because the polymorph spell goes on to explain the ways in which the change is still restricted but the polymorph any object spell does not explain the ways in which it is restricted means that the polymorph any object spell is no longer bound by the limits of the polymorph spell may be a case of the reader bringing the reader's own expectations to the text: That is, because the polymorph spell removed some restrictions from the alter self spell, so must the polymorph any object spell also remove some restrictions of the polymorph spell.
But the polymorph any object spell, in fact, does remove some restrictions of the polymorph spell. However, instead of, for example, granting the new form a creature's extraordinary and supernatural abilities (which, to be clear, the polymorph any object spell does not grant, and it would be a very big deal if it did), the changes wrought to the polymorph spell by the polymorph any object spell are in the latter spell's targeting (it's pitch: "Now you can affect nonmagical objects plus deathless, undead, and constructs—but, no, still not plants"), range, and duration ("You figure it out"), and that the result can be either a creature or an object ("Just don't try to make bank and something something special materials something").
Nonetheless, the polymorph any object spell's mechanics—the details of what creatures can result from it and what creatures keep from their original forms while in their new forms and what creatures gain and lose due to their new forms—remain as per the polymorph spell because the polymorph any object spell does not say that it modifies those mechanics of the earlier spell—and because it says that other than exceptions that it goes on to note that the polymorph any object spell "functions like polymorph."
An Aside: Consider, in context, also shapechange
The 9th-level Sor/Wiz spell shapechange [trans] (PH 277–8), in part, says, "This spell functions like polymorph, except that it enables you to assume the form of any single nonunique creature (of any type) from Fine to Colossal size." It goes on to—in addition to other changes to the earlier spell—increase the HD limit imposed by the polymorph spell (up to 25 HD), allow gaseous and incorporeal forms, grant the subject the new form's extraordinary abilities, and grant the subject the new form's supernatural abilities while removing the subject's own. (These aren't normally lost when the subject of a polymorph spell.) The polymorph any object spell lacks completely this kind of text, and it's this kind of text—that makes specific modifications to the earlier spell—that's necessary to modify or remove the restrictions imposed by having the polymorph any object spell function as the polymorph spell.
An expansive reading of the polymorph any object spell's opening description—for example, "'This spell functions like polymorph, except that it changes one object or creature into another" to every extent with no limits'—empowers the polymorph any object spell well beyond the higher-level shapechange spell.
"Why is this an 8th-level spell?"
I can't know why the designers opted to make the polymorph any object spell an 8th-level spell. However, I've DMed for PCs that wielded the polymorph any object spell, and I can vouch for its versatility and problem-solving acumen. In practice, the polymorph any object spell like the 9th-level Sor/Wiz spell wish [univ] (PH 302–3) except that the results are mundane, and, in some ways, it's more fun. (It requires material components found in any spell component pouch, and it costs no XP to cast, so it can be cast capriciously and whimsically.) No, the polymorph any object spell won't grant the resultant creature a typical form's spell-like or supernatural abilities nor many of its extraordinary abilities, but it can change a pebble into a living creature (even a plant!) with up to 15 Hit Dice, change the party fighter into a firbolg (Monster Manual II 101–2) permanently (i.e. until dispelled), and turn a vampire (MM 250–3) into a rowboat (but not into a barghest, iron golem, mummy, treant, or adamantine sword). That's really not nothing.
Sure, this means that the polymorph any object spell pretty much only results in boring creatures and objects, but, y'know, most of the universe is boring, so, in that sense, the polymorph any object spell still commands my respect as a DM. If, in your campaigns, you find that the polymorph any object spell is underperforming compared to other 8th-level spells, I'd humbly suggest lowering the spell of level of the polymorph any object spell rather than increasing its power: even bound as it is to the polymorph spell, I'd imagine it'd quickly become, for example, an extremely popular 6th-level spell.
