Hello there! Today I came across a mud sill that was built up to 2.5" in some areas and have never ran into this. My thoughts are that this was done to level a bad (or past sinking crawlspace) foundation.
I think if you plan on instructing them to “Monitor”, you best be prepared to outline the procedure to do so, and what to do if monitoring leads to other instructions on what to do from there…
Assuming that you did not see a problem such as the mortared sill crumbling or failing in some way and do not have a reason for it to fail, then it is just an observation.