I don't have anything but anecdotal evidence to rely upon, but here goes.

I have worked in darkrooms with multiple enlargers, where some use below lens filters, and others use above negative filters, and have seen no difference in results.

I have gone from using a below lens filter enlarger to one with a multi-grade head, and can see no filter induced degradation in the earlier prints.

It doesn't surprise me that this would be the case - the role that a below lens contrast filter plays in an enlarger's light path is very different than the role that a camera filter screwed on to the front of a lens plays.