[Solomon Parker]

I've read several places that the center to center spacing should be 1-1/4 inches and you should trim the sidebars down from 1-3/8 which is typical to 1-1/4.

Can be, not necessarily should be, it's up to you. There are some benefits.

Will this create difficulty for bees, particularly the queen and drones to move between the top bars into the next hive body? If sidebars are trimmed to 1-1/4 inch, does that not reduce the top bar spacing to 1/4 inch?

It depends on the frames you start with. With foundationless frames from Kelley, you'll have a narrower space, which could cause problems. But I use those frames for drone, so I don't trim them. I do trim Mann Lake PF-120 frames which have a narrower topbar and so there is no problem. As someone mentioned, if you are concerned, you can trim a wood topbar 1/32" off each side and you should be fine. Watch the fingers.