The power and volume buttons that you see on the sides of the phone are part of the back cover. When you separate your phone the buttons stay with the back cover. The actual electrical button is on the mid-frame with the display and motherboard. They look to be stuck in place with adhesive.
The case buttons are held in place with a small metal tab that is stuck in place with adhesive to the back cover. You can pry it up just enough to allow the button to be removed but not so much that the adhesive is destroyed.
I removed my buttons to file them down so they didn't stick out so far and to soften the edges. Everything came apart and when back together easily. Be careful inserting the mid-frame back into the cover, there are lots of spring contacts for antennas and other things that are part of the back cover.
Re-reading your post, I don't think the electrical buttons are part of the motherboard. I've seen videos that show the motherboard removed from the mid-frame and I don't see the buttons. They must be on a cable somewhere but I don't know for sure. I didn't disassemble my phone any more than necessary to access the exterior aluminum buttons.
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