Yes, I turned the small sides in. I found I liked the fit better with the short sides inboard towards the strut body.
I found that if I reversed the bushings and centered them in the arms, I ended up with too small of a gap where the strut knuckle fit between the two bushings. Of course, since it's just rubber, I could have forced the bushing centers apart a little and forced the strut body between them, but I figured if things lined up naturally without having to do that, it would be better.
With the small sides in, when I centered the bushings in the receiving cylinders in the arms, it worked out almost perfect such that the distance between the two bushings was very very close to the width of the strut housing. Seemed to perfect to be coincidental.
So I don't know if they were really designed to be that way, but it worked for me. And if you're seeing the same small difference on OEM bushings as I saw on aftermarket MOOG, then I'm starting to believe it really might be intentional. Hark... Did I stumble across something that isn't even in the repair manuals??
If you haven't already pressed your old rear bushings out yet, measure the distance between the two of them, and compare that to the width of the strut body.
As for how to fixture the press... I've done so many press operations over the last few years that I don't remember specifically what I used, but it was probably a long bolt passing through one of the bushings to press against the other bushing. Either that, or I managed to fit the control arm down between the parts of the press and straddled the anvil? I don't think I have enough room on my press to fit the arm down inside, so it was probably a long bolt. Something just a little smaller OD than a spindle pin.