This PrusaSlicer project cuts the original 3DBenchy.stl into parts, using 100% infill density for the aft hull and 10% lightning infill elsewhere. The resulting model floats upright when printed in PLA. This version is under 9 grams, but some of my previous test prints were over 12 grams and just barely floated, so there are many solutions to this problem.
I used PrusaSlicer 2.6 because its "center of gravity" visualization is somewhat useful.
The "Public Domain" license only applies to the slicer profile, as I didn't create the model.
What exactly are your modifiers modifying?
Edit: oh, I see. A modifier lets you draw shapes onto the model instead of cutting planes only. That does seem like an easier approach.