Natural weapons are weapons that are physically a part of a creature. A creature making a melee attack with a natural weapon is considered armed and does not provoke attacks of opportunity. Likewise, it threatens any space it can reach. Creatures do not receive additional attacks from a high base attack bonus when using natural weapons.
-- The description of Natural Weapons in SRD
Since unarmed strike DOES NOT considered armed and does provoke attacks of opportunity (if without the feat), DOES NOT threaten any space it can reach (if without the feat), and, most importantly, DOES receive additional attacks from a high base attack bonus (regardless if with the feat or not), it is quite obvious that unarmed strike is not and never has been considered as a natural weapon (otherwise, you can simply use it as a secondary attack and take -5 penalty regardless what other stuffs you are using in your full attack) and hence is a manufactured weapon, even though it is not actually "manufactured".
But in the description of Magic Weapon, it says
You can't cast this spell on a natural weapon, such as an unarmed strike (instead, see magic fang). A monk's unarmed strike is considered a weapon, and thus it can be enhanced by this spell.
-- Magic Weapon
So it is again considered as a natural weapon, regardless of its features showing that it is not.
On the other hand, it also says that
Some creatures combine attacks with natural and manufactured weapons when they make a full attack. When they do so, the manufactured weapon attack is considered the primary attack unless the creature’s description indicates otherwise and any natural weapons the creature also uses are considered secondary natural attacks. These secondary attacks do not interfere with the primary attack as attacking with an off-hand weapon does, but they take the usual -5 penalty (or -2 with the Multiattack feat) for such attacks, even if the natural weapon used is normally the creature’s primary natural weapon.
-- The description of Manufactured Weapons in SRD
I looked around and, while there's no example in MM, it seems nothing prevents any creature to do more than one attack in a natural secondary attack if it can use it to do the same as the natural primary attack. The only reason the existing monsters can't do it is that they don't have a natural attack that can attack multiple times (as per the rule, they are not allowed to do so without using unarmed strike).
So, combining all those things together, does that mean, Rule As Written, the following is possible:
A monk wielding a quarterstaff, using it for two-weapon fighting, and also using unarmed strike as her "secondary attack", which is a natural weapon that is allowed not to obey the rule of "do not receive additional attacks from a high base attack bonus". And it also seems that the Flurry of Blows does not prevent her using unarmed strike with highest BAB for twice. So the following attack sequence happens:
(Occupying both hands with quarterstaff just to avoid making things over complicated. I guess someone may argue that I cannot use it as the secondary attack if I use it as part of primary attack (either main-hand or off-hand of the TWF sequence))
+13/+8/+3 (Quarterstaff, main-hand)
+13/+8/+3 (Quarterstaff, off-hand)
+13/+13 (Unarmed Strike, flurry of blows. I wonder if TWF penalty should be applied since nothing says whether it is main-hand or off-hand, but let's say it is main-hand for now.)
+10/+5/0 (Unarmed Strike, secondary attack so granted for free; -5 because of being a secondary attack, but the -2 penalty of TWF does not apply since the rule says it only applies to the "Primary Hand" and "Off Hand" attacks)
So it is supposed to be 11 attacks in total before any magic or feats get involved?
And, if a monk can do the unarmed strike in both main-hand and off-hand in TWF (which seem to be what most monks are doing), does that mean there's no limit of the times to apply an unarmed strike in a full attack and a secondary attack of unarmed strike (for free) can also get involve? (Which is just replacing all quarterstaffs in the above example with unarmed strikes, and still keeping the secondary attack sequence also with unarmed strikes.)
PS. I have seen people discussing this like this one:
But it doesn't seem to have an answer anywhere describing the situation when a monk (or even a non-monk) what an unarmed strike is and what it can do exactly that can satisfy everyone. Is there an errata for this?
It took some time for me to figure out how to find the article from webarchive, since some links and the search function does not work there.
While still not quite satisfying, these do provide additional details.
So the conclusion is:
- Unarmed Strike/Unarmed Attack is neither manufactured weapon nor natural weapon, so the rules like "can be used as a secondary attack" do not apply to them. The best you can do is to use it as an offhand attack.
- For the weapon enhancement purpose (and for that purpose only), the Unarmed Strike/Unarmed Attack is always considered as a natural weapon, if you are not a monk.
- On the other hand, a monk can take this as both a natural weapon and a manufactured weapon. Those articles keep using examples of taking unarmed strikes as off-hand attack in TWF but never explain if it can take as a secondary attack in the form of natural weapon if the character is a monk, leaving the question unanswered.
(It seems, though, that the unarmed strike cannot be used as a secondary attack, even for a monk, and is always considered as manufactured weapon in this case scenario. But the author never points this out in those articles.)