I was also concerned about that. Actually, our AC leaked and I took it to Crossroads and it wasn't sealed for that very reason, but the AC is on the peak.
Our fan is offset enough on the roof that it didn't cause me any issues. Your bath looks like it is in the same place from the layout Crossroads posted.
I figured If they got the fan/vent secured and sealed you have up there now, you shouldn't have any issues. Just plan for a full day when you have dry weather. I bought an install kit with my fan here -->
http://www.amazon.com/gp/product/B00...?ie=UTF8&psc=1
Assuming you have the beige roof, you will also need a tube of the Dicor almond self leveling lap sealant for the job.
There are few videos on youtube that walk you through the job. I have the Maxx Fan, so I watched this one.
__________________
2017 Ford F350 Super Duty 6.7 King Ranch Crew
Sold the 2016 Crossroads Sunset Trail Grand Reserve 32BH
2020 Grand Design Momentum 320G