When layer or layout scale goes below 0.01, it becomes invisible

IIRC there were some bugs using close-to-zero layer scales, and to fix them rendering is skipped if the layer scale is extremely close to zero (less than something like 0.0000000000000002). Using such tiny layer scales seems bizarre to me, lots of things will probably be broken if you scale in to that range anyway, as math calculations end up producing zero or infinity results.

I see, but 0.01 is pretty far from 0.0000000000000002. This limitation makes some C2 projects incompatible with C3. It should probably be safe to allow scaling down to 0.0001 or even 0.00001

I can't find any other limit in the source code, so I don't know why there would be a change at 0.01 specifically.

That's odd. You should file that as an issue.