At least on #3 there's a very clear answer that was foreshadowed in almost excruciating detail in the story:

"You don't see nice ways to do the things you want to do," Harry said. His ears heard a note of desperation in his own voice. "Even when a nice strategy would be more effective you don't see it because you have a self-image of not being nice."

"That is a fair observation," said Professor Quirrell. "Indeed, now that you have pointed it out, I have just now thought of some nice things I can do this very day, to further my agenda."

Voldemort quite clearly said that he is going to do something altruistic that will further his own goals. The only altruistic thing he did up until becoming a jewel was to resurrect Hermione (as he has promised by that point) and give her regenerative abilities.

Do these further his own agenda? Most certainly; he would want those abilities for himself as well, but may not have known whether or not the rituals would work. This is quite clearly shown by his jubilations when the Stone of Permanence made permanent the Trollification ritual and his Diffindo used to test the results.

To Voldemort Hermione's superpowers are barely worth noting: She has the killing intent of a bowl of wet grapes, isn't particularly powerful in her own right and is still weak to Fiendfyre and the Killing Curse, both of which Voldemort handles with such ease that he makes them look like a staple spell from a first year student's spellbook.

Also if you really want to go digging deeper into "who benefits", then Voldemort may have expected that Harry might need to be stopped by someone who knows EVERYTHING he is planning. Conveniently Harry is bound to a vow to honestly confide in Hermione before doing anything that might endanger the world. Now if Hermione is impervious to anything Harry can do (he probably cannot cast the Killing Curse and will not be capable of handling Fiendfyre in years) it means that Hermione is perfectly suited for being an extra stopper to Harry's dumb plots.

The first point is, in the end, probably idiot balling on Voldemort's part and more or less the same applies to the second point, but I think number two can also be possibly made impossible by limitations in the unbreakable vow as any sentence that begins with "Also..." doesn't really belong in the same thought as the earlier parts of the vow, so perhaps it would've been possible, but with a different vow. Even then it's a bit too overpowered for an unbreakable vow and may trespass on some limitations that EY has himself thought of for it.