Yes for Objects, No for Creatures

Note that the Specter's Incorporeal Movement feature does not specify that they take damage if they end their turn inside a creature, only an object.

As for dealing with Objects, yes...a Specter may choose to take damage in order to stay inside of an object and yes, that will give them cover based on how much of them fits inside of it. If they are parked stuck through a table...that's probably half cover. If they are completely inside a wall, that's Total Cover.

As for dealing with Creatures...

The Specter's Incorporeal Movement feature has nothing to say about ending its turn inside a creature. The standard rules for this (on PHB 191) say...

You can move through a non-hostile creature's space. In contrast, you can move through a hostile creature's space only if the creature is at least two sizes larger or smaller than you. Remember that another creature's space is difficult terrain for you.

Whether a creature is a friend or an enemy, you can't willingly end your move in its space.

As always, specific rules beat general rules, but in this case...there are no specific rules overriding that final statement.

Thus, in the case of dealing with another Creature...a Specter remains bound by the same rules as everyone else because its Feature doesn't say otherwise. The same way that a Halfling can move through the space of a creature that is only one size larger than it, a Specter can move through another creature's space regardless of size. But neither of them can willingly end their turn in another creature's space.

A magic weapon that possesses both the brilliant energy and ghost touch magic weapon special abilities ignores nonliving matter yet affects incorporeal creatures normally. Further, according to this Paizo blog post, a weapon that possesses the quality trip—like a halberd or whip—can also be used to perform the combat maneuver drag.

In combination, a creature using, for example, a +1 brilliant energy ghost touch whip can take a standard action to make a combat maneuver check that provokes attacks of opportunity against the square that the creature thinks her foe occupies. She makes a normal combat maneuver check against the foe's combat maneuver defense to drag her foe except that, because of the foe's total concealment, the drag maneuver has a 50% miss chance. If she's successful, she'll pull that incorporeal creature out of its space within the object to the adjacent space where the incorporeal creature can be dealt with normally.

Note, however, that a +1 brilliant energy ghost touch whip—despite costing 72,301 gp—is useless against incorporeal constructs and undead. You'll need a different tactic for ghostbusting or Vision-wrangling.

Of course—because Pathfinder—, casters can do this better: a similar weapon can be conjured with the 2nd-level spell ghost whip.

Note: I look forward to other answers. This is an already complicated problem made worse by the incorporeal creature having total concealment provided by the object! Also, thank you, ShadowKras, for suggesting the ghost whip spell.