The Md inspection is for safety and compliance.
They are particular about safety. For that they
will check brakes, lights, tires, chain, windshield
(if present), aim of headlights, reflectors (particularly
on forks), frame and forks not bent, chain guard, loose
or missing spokes, passenger foot pegs if it has a
passenger seat, bearings and tree ok.
For compliance they will check light on license plate,
exhaust system (the certification stamped on the pipes,
but they may let this slide), ape hangers under 18"
no fluid leaks, 2 mirrors, VIN not altered.
They don't care about things like ragged seats, rust,
dents in tank, current inspection stickers from other
states, accessories, power commander etc, aftermarket
lighting (as long as it is compliant or can be turned off).
They will do a test drive, so it should run ok.
It's a pretty thorough inspection. It is basically the
only time it gets inspected so they want it safe. They
are really doing you a favor if they catch something
that needs to be fixed.
If you want to slip something by the inspector,
best to make the change after you get the plates.
The minimum thickness is supposed to be stamped on the rotor somewhere. (I haven't actually looked for it.) I doubt they would take an actual measurement if the rotor wasn't worn obviously thinner. I would expect them to check it if it was worn. On a bike with dual disks (same wheel), they would expect the pair to match in thickness, but probably wouldn't fail unless one was under specification.