Do you fill the tank with a pump that dumps fuel in from the top? Unless you were intentionally aerating the fuel (which you wouldn't be doing), you shouldn't have any bubbles at the pick-up tube.

There are issues with the efficiency of the polishing system. I think that going way to high a capacity is less effective.

I just had a Racor FPM 50 installed. We are using a dedicated Racor Filter, using the engine pick-up line (by teeing off) and connecting the return line afterwards.
I would have been concerned with the possible short-circuiting of the pick-up line to the engine feed EXCEPT that the RACOR FPM has such a low rate of flow. (It's about 2 gallons per hour.

In your case, Max. I would be careful if you're running the polishing while the engine is running if you have a very robust pump.
If you are polishing only when the boat is at the dock or sailing -- vs. when the engine is on, then it wouldn't be an issue.