If the vent is new and its seals are not damaged, it seals pretty well. If yours is old and tired, you might want to replace it; new vents are not particularly expensive. Use butyl tape to seal it, or Donna will give you a talking-to.
However, several Compact Jr owners have reported that the roof of the popup section, which should have a slight upward arch, sags; and of course, Murphy's Law says that the low point of the sag occurs at the vent, so that water puddles around the vent and gives its sealing properties a real workout.
Several owners have added internal ribs to the popup to restore the arch, either bolted-in or fiberglassed-in. Restoring the arch raises the vent to the high point of the roof and water drains away from it rather than toward it. It looks as though you're doing a considerable amount of work on yours, and you may want to take a look at the popup roof and see if you ought to do something similar.
Some searching on this forum ought to turn up some pictures of fixes; I did my sister's Compact Jr using electrical
conduit as ribs, and it's shown in one of my "winter fixup" threads.
Edit: Here are a couple threads discussing the subject:
New Modification To C-J
Compact Jr popup fiberglass