When the darkness spell description says, "If darkness is cast on a small object that is then placed inside or under a lightproof covering, the spell’s effect is blocked until the covering is removed," it's explaining to the reader how the rules deal with the fact that this isn't an ordinary area spell.
Ordinarily, a spell that has an Area entry radiates outward from a point of origin, a grid intersection (or, if you prefer, a crosshairs) that was picked by the caster when the spell came into effect. (See also Aiming a Spell on Area.) In addition to cluttering the battle mat, that point of origin also determines how—or even if!—the spell's area extends past any obstacles in the area.
However, unlike normal area spells, the subject of the spells darkness et al. are objects, and those spells' areas radiate from the objects that were their targets. That makes these spells' areas more sensitive to interaction because they're usually small and mobile. For example, while a 10-ft. cube of butter (or whatever obstacle you prefer) can be dropped onto a point of origin to squelch an ongoing area spell—making it so every angle from the spell's point of origin is occluded by an obstacle—, it's far easier for a sneaky halfling arcane trickster to cover with his hand a coin on which he's cast the darkness spell. Even though creatures aren't usually obstacles enough to interfere with a spell's area, covering the coin, were told by the darkness spell's description, nullifies the darkness spell's area until the trickster uncovers the coin.
So the description of the darkness spell is here adding rules that, in an extremely rare display, we might go so far as to call as common sense: A dude can put in his belt pouch a rock on which has been cast the darkness spell and, even if the GM would've normally ruled that a belt pouch is an insufficient obstacle to block a spell's area—which the GM normally should—, here, because of that explicit text in the darkness spell description, that belt pouch blocks the darkness spell effect.
Question: What if a caster picked as the target of the darkness spell the bottom of a wall?
Answer: Because the question asks specifically how folks would rule on this, here's how this GM would rule: He wouldn't let a caster pick that target. Nobody really liked my answer as to why I wouldn't allow it, but I don't care: Allowing it makes my brain hurt with all the cascading gamewide implications. That is, the spell says, "This spell causes an object to radiate darkness," so if in your campaigns you want glowing houses or shadowy houses, then go ahead and allow structures or parts of structures to count as objects. In my campaigns, I just don't allow such spells to target structures or, for that matter, individual parts of things (e.g. a foe's mouth, one tile of a tile floor).
Q: Okay, but if the GM were to allow a caster to target a wall with the darkness spell anyway…?
A: It's possible the entire structure radiates darkness—the wall and everything it's attached to shedding darkness to the limit of the spell's area. Alternatively, that lone brick that the caster picked that's part of the wall sheds darkness, and if that brick is the same brick on the wall's opposite side, then there will be darkness there, too, albeit occluded by any bricks above or below. (Unlike a spell with an effect entry, the caster doesn't need to see the entirety of an area spell for the spell to come into effect successfully.) However, if you don't like either of those options, though, then you'll have to make up something.
