certain builders cut domes to whatever deck height you give them, some dont. Sounds like Mat suggested the modquads cause for what your doing there prob ismt much to be gained from him cutting some from what it sounds like.
Easy fix now do this:
1. remove cylinder
2. clean up and put silicone of choice as a gasket at base
3. torque and measure deck height for reference
4. measure step in domes for reference the install
5. recheck squish
.040 is optimal but .050 is fine also.
when measuring the deck height, and step add them together the usually .010 for the orings. theres your squish without bolting up.