I have two mode which using the cloud compare for comparing those together, i used the ordinary distance compare method ( C2M signed method) with this parameter as you can see here:
and for more details i tried also the M3C2 method by this parameters:
but there is difference in output as you can see:
So i think it comes form the M3c2 setting (which one is reference ,cloud #1 or cloud#2?!).
I have tried to give the reference stl file as cloud#1 and target to be compared as cloud#2 as at export part as projection core points on cloud#2 i have tried projection core points on cloud#1 but i have get the same output and it project the colored compare results only on the reference cloud which is Cloud#1 !.
i have tried to use cloud#2 as reference and the M3C2 parameters are this kind now:
and the colored output shown on the target stl mode as you can see here: