Is it even possible to reinstall the strut mount onto the strut assembly wrong, and still have it match up to both the steering knuckle and upper body mount holes? There are basically three ways that the mount can match up to the upper holes where it shows from under the hood (in the engine bay) and I'm just thinking this now after spending the day replacing my struts and mounts. I think I'm being paranoid here, please reassure me that I am.

 

I've done the rears on my 1993 es300, so maybe this won't be of any help since you have a different car and are talking about the fronts. That said, and your concern is with the top mounting bushings, mine had a small angle to the rubber to match the slight inward inclination of the spring when seated. I don't recall exactly, but I seem to remember the mount holes being slightly offset so it would only go in one way. If yours are all equidistant from the center, then I'd say the manufacturer's intent is it makes no difference which way it goes in.