It's pretty hard to get silicone completely removed and if any is there it will make a good release agent. I don't think mineral spirits will cut it very well. In this case, it was not the silicone that failed and Casita
recommends using silicone. Plus, you were able to get it apart to replace it.
I'd say do it with silicone, as Casita did and recommends. Easy to get, cheap, available in small tubes to reduce waste, can be re-done later if needed. You can also get paintable silicone which acts exactly like regular silicone, but can be painted. Good stuff.
The main place you might want to avoid using silicone is on an area that might get a glass repair or paint later, but you already have silicone on this spot, so no problem.