Your tile substrate should be smooth and plane. To install a
membrane over an irregular surface in an attempt to shortcut any other preparation wouldn't be adviseable.
Once the surface is smooth then the membrane can be applied.
The only other suggestion would be to use a Self Levelling Compound but don't forget the related primer.

This is not to say you absilutely cannot go directly over the existing
thinset surface, it just depends on how rough that surface is now. The surface can be sanded mechanically using a floor machine or a floor grinder.
