Welcome to the forum.
I am not familiar with your coach but this is very strange.
Of course these plumbing vents (360 style or the cap style) are intended to be mounted over a plumbing pipe stack (black or grey tank vent pipe stacks specifically). This situation almost looks like a factory goof (not sure if 360 style vents are factory supplied typically or not on new rigs), where the stack roof opening was made in the wrong place and someone stuck this 360 vent over the roof hole. Of course some rain/water can still penetrate the vent screens on top and without an actual plumbing pipe stack there.....the water is going to get into the roof space. You definitely want to get this resolved ASAP by having all vents inspected and confirmed correctly installed.....over an appropriate plumbing vent pipe stack. In the mean time, you need to prevent any further water getting in through this vent screen. If the others are legitimate plumbing stacks then you don’t want to block them off.......you can usually use the quick smell test (while on the roof) to verify they are actually connected to your holding tanks.
It would also be worth contacting Thor with your pictures and obtain a plumbing diagram from them which shows where the factory stacks are “normally” located on your roof. If this is a “normal” location, the next question is where is the plumbing stack? It will be interesting to know what has happened here.
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