Well a couple things. First off, the ls50’s as I understand them, are excellent nearfield speakers. Not intended for high output, or having great extension(deeper bass), but known for uncanny imaging in a close setting. That’s an expensive pair of speakers to use as upfiring that could make a real nice 2.0 or 2.1 office setup.
Also, you can’t just use any regular speaker as an upfiring speaker. Actual AE(Atmos Enabled) speakers have a notch in the frequency response that helps trick the brain into thinking the sounds are coming from overhead. I would consider returning them for something else, or use them as a nice desktop pair.
For rear heights, it looks like the minis are smaller than the 90’s. So to my eye, they should fit. If not, you could lower the surrounds a tad, and install a couple of small shelves. A problem with the minis is the same as the ls50’s. They’re a regular old speaker.
In any case, setting up AE speakers is tricky. Getting the right angle so the sound bounces where you need it to will take some time.
So imo, it’s worth exploring Atmos, but some different speakers will be in order.
Edit: I thought I was looking at the “minis” but realized I was not. Can’t find them so maybe a link?
How was it you decided on the ls50’s and the minis? Very different speakers from each other.