You'll have to excuse me, but going into the wayback machine for these thoughts. Haven't used an enlarger for 30 years, but I assume the technology is the same.
Beseler enlargers have a tray, not only above the lens, but above the negative and the condenser. I don't believe I ever used it or gave using it any thought. Now that you bring it up, that might be better as you're coloring the light source before it hits the image. But, like I said, I always used PC filters below the lens unless I was using an enlarger with a dichroic color head. With that head I could dial in the PC filtration at the source.
So, I guess, all things being equal, above the lens is probably marginally better, but below the lens works just fine. Sounds like you've got other considerations like hardware on hand, modifications to make it fit your system, etc. I'd say go with the path that makes most sense with your configuration.