I covered our previous trailer for 11 years (Adco cover) and used foam pipe insulation where ever I could to prevent tares I used towels to cover the TV antenna and those spots that the foam pipe insulation would not work. No tares for years, but tares did develop eventually in a few spots. The tares did not get much larger over the years, and the new owner is still using the cover. I would not remove the drain extensions, protect them with foam or what ever works and be careful when you are putting on or taking off the cover as it will catch on the corners and you will tear off the extensions.
2017 Cardinal 3250 5th wheel
2016 Ram 3500 Crew Cab long bed with Aisin Transmission