I have both above and below sets.

The below sets will not affect print quality. i.e. they are just as good as above the lens filters. But, and its a big but, the unit that fixes to your lens does just that and depending on your lens it may obstruct the open up / close down lever. It can make changing aperture difficult, The unit will not fit on larger diameter lens such as those for 4x5 unless the max aperture is really small and hence the lens barrel is small diameter. Then if those under the lens filters get scratched or finger marks (chemicals) or dusty then they will affect image quality. None of these things are potential problems on above the lens filters on diffusion enlargers where the filter is above the mixing box. Scratches could be a problem on condenser enlargers depending where the filter draw sits. Also if you are printing 35mm on a 4x5 enlarger and are using a recessed lens board, the unit may not fit.
If your enlarger has a filter draw I would use above the lens filters for the above reasons. But if no filter draw then below works fine. Just take very good care of the filters. And check the unit will fit your lens before you buy it.