Transitioning between 90 and 100 ohm diff pairs using coupling caps?
What you've described will cause an impedance discontinuity and will negatively affect signal integrity, qualitatively speaking. That is, at the point (assuming for this particular instance the connector is neglected) your SoM meets the PCB, there will be a discontinuity from 100R to 90R and you will get some degradation of your signal, which for USB 3.0 would likely manifest as a shrinking of the eye.

It's important to understand where your routing requirements come from. Silicon vendors are not necessarily the system integrators who are not necessarily the PCB designer and they can (and do!) issue conflicting requirements on what to do with your design.

Your FPGA SoM vendor assumedly has in-depth knowledge of the FPGA on their device. They believe that routing 100R was the correct choice for the differential pairs and the transceivers on the device. 

In this case, what FPGA are you using? Do they have an application note on applying their transceivers to USB 3.0 usage? What are those pairs being routed too on your host PCB? I would start with what the silicon is expecting or requires, and try to provide it a channel that meets that need. Without knowing more, as you have originally posted with having an FPGA SoM with known impedance, I would match that on your board.

Also, keep in mind the tolerance of your PCB; +/-10% tolerance on a 100ohm line is already a big number that gives some wiggle room as well.