Again, old issue - roof warranty after 1 year is only the material warranty. Meaning, they guarantee that material won't disintegrate for 10 or 12 years, whatever it says there. And it won't indeed disintegrate for about that long. This warranty doesn't cover mechanical damage. Chances of 303 to cause disintegration of synthetic rubber are zero, it just doesn't happen. This stuff is washed off with rain every winter, and next spring nobody would even know whether there was any treatment.
Btw, my roof was covered with some goo right from the dealer, they treated it with something few weeks before I bought it 'cause it was sitting there for almost a year.