Oh gosh. Nightmare. I see why you were worried now. The thing I learnt recently about roof tiles, is they're not expected to keep all the water out. That's why you have felt or a breather membrane, to catch any residual water that seeps through the tiles. Ours was worn out and water came through... this is how I know.
I guess that's why they didn't think the crack in the tile mattered. Sound like a nightmare bunch of workers though.
No one is allowed in our house full stop. This is agreed at the point of assigning people the work. But I get how access to the toilet is an issue in this case. We've not had anything complex done.