Figured it out. There were mangled studs separating the backplate and barrel plate, so the hammers were further from the keycaps than God intended. This lowers the tactile point and raises the effort to press a key. (ie, your bolt-modded board will feel like a bolt mod candidate whose backplate has separated due to lost rivets.)
You can use a rip-o-meter (a stack of 5g nickels) to measure how much force a key will support before it begins to move downward. In a healthy model M, it takes nine or ten nickels to start the key moving, because the spring is compressed to ~45g at rest.
If there's a gap between barrel plate and backplate, the spring is less compressed at rest. My guess is that fewer than nine nickels will start that key moving.
(This is assuming every M has springs with identical spring constants.)
If this test works, you could detect lost rivets without opening the case.