@Keet
Your approach presented here is brilliant!
Basically, you need to make a negative of the hole you need.
Then you subtract it from the main object. Brilliant!
I've already done a few tests, it's not exactly simple but not impossible.
The result is acceptable.
This way, part of the smoothing can be solved (using a cylinder, torus, or some of the modeling library).
A tip: save and reopen the application from time to time. Will free the temporary memory.
This gave me the opportunity to discover a few more tricks.