I noticed what compared to ldraw parts and also a diagram of a lego piece that the studs on mecabricks ate just a bit too tall, this is not an issue on most bricks, but on things like heads this can be a very large difference.
Could you specify how much taller they are? Any comparison images? Scrubs has been working on this project for seven years so I think he knows pretty well what he is doing, since he's made almost all parts himself. Here's some rules he set up for part modelling: https://www.mecabricks.com/en/forum/topic/15
Ldraw system is not always accurate to the real world. They chose 1.6mm I believe for the stud height while Mecabricks is using 1.8mm. The real dimension is somewhere around 1.75mm. The same goes for anti studs. They use 1.6mm while real depth of the cavity is 2.1mm
Ldraw is a system and they have their own convention and unit. On Mecabricks I try to be closer to real dimensions.