I don't see why the cutting into the top wouldn't work. Or, instead of cutting into the front - cut out a rectangle a little bigger than your machine - give it more space in front, so you can move your machine back when you need to change the bobbin. I have an old office desk that my DH did that for me. I do have a machine with a drop in bobbin, so I don't have the problem of changing bobbins.
I did have to do away with the drawer under the cut out, but with all the other drawers it has - I've had no problem finding new spots for the stuff that was in there.
I also, never bothered with a plexiglass piece to put around the machine.
Just do what works and enjoy it!