I guess because the bookshelf is a smaller speaker, and so much flows through it in home theater. I just figured it couldn't take it. That's wrong?

It is only capable of playing what it was designed to do, no more no less, whether it is a center or Left or Right makes no difference. The only way you could damage it would be to physically smash it, play clipped signals through it or have it play far beyond its power rating, like 1000w for a length of time and over heat the voice coils. The fact it is a center doesn't matter.

Vertically configured speakers can have better horizontal dispersion than horizontally configured ones. Horizontal center speakers are intended to meet an aesthetic or space requirement for that arrangement. They have no other benefit and I don't use them. Carry on with the M3 there.