The reason is, it's hard to get all the polishing compounds out of the seams (where the caulking goes) in order to get a good positive seal after polishing. Also if there is any loose old caulk, it may vibrate out during polishing and get in your pad which will scratch your aluminum. The weather stripping is bigger and easier to adhere to a cleaned off surface after polishing and it won't get dirty during the process.
As far as removing plastic vent covers, ours were very old & brittle. We started off with them on, but when the compounder touched them it shattered little chunks off. So we ended up removing the old ones and putting the new ones on, then removing them again when it was time to polish in that area again so they wouldn't get damaged or soiled. We covered the opening with taped on plastic tarp so the debris would get in the trailer.
We also removed all the plastic lenses, etc so they wouldn't get damaged and so we could get in real close with the buffer. It's a pain, especially if you are using your trailer while going through the polishing steps like we did over the course of a year or so, but worth it!
Absolutely, remove all plastic parts before stripping the clearcoat (if you have it) because most strippers will melt the plastic.