Harrison, I think you should be ok. You're right that the plate position is dictated by the tiny locking tabs on the lower half of the MX switch housing, and the PCB is flush with the bottom of the switches. I'd recommend just to be careful on the first few you solder back in, to make sure the switches sit flush on the PCB. Replacing keys in 2 passes (like I did with KL's board) makes this a non-issue.
The Filco tenkeyless doesn't appear to use any standoffs, other than the switches themselves.