I've literally never had this happen with a toilet made this century, but if you're buying one it doesn't hurt to check the MaP rating.
If your printer has a touch sensor, then raising/lowering the entire bed has no effect on the first layer. The Z offset defines the difference between the touch point and the first layer.
I think most people calibrate the Z offset for 0.2 mm, and then never change the first layer height.
Edit: oops, this thread is a month old.
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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.
So you're saying it's technically a pirate ship?
You can see in the photo that the wall is just above the waterline. It stays in that orientation until you disturb it enough to spill water over the edge, at which point it capsizes.
It's not rocket surgery. Boats need more weight at the bottom than the top. If you put it in water and it leans, shift some weight in the other direction.
PrusaSlicer has a 'center of gravity' indicator that removes at least some of the guesswork.
The technique can be applied to other models: Use PrusaSlicer's 'cut' feature to break the model into parts, and tweak the settings (mainly infill and perimeters) to give each part the desired density.
Lock some calipers (with a rod sticking out) to 1.5mm shorter than the part height, compress it down onto a kitchen scale until the rod is just touching the platform, and record the weight.
That's just the first procedure that came to mind. I will try to think of a way to do a hook strength test today.