I have a thule rack mounting system for my 2010 fit and I'm curious if this will work with the OEM rain deflectors for the windows?

 

I don't see why it would cause any problems. The clip goes on the weather strip side of the window frame and the rain deflector is attached to the outside of the window frame.

I would be more concerned about the rubber door seal. I had a Thule rack on my old Accord and it eventually ripped the weatherstrip on the rear door.

 

I'm concerned about that as well. I'll have to keep it well moisturized. Thanks!

 

I forgot to mention that the car was 14 years old when the rack was first installed and it ripped the weatherstrip when the car was about 17 years old. Maybe its just old age in my case.