If you are willing to switch to Pipewire, try EasyEffects, it might work better as it's based off of pulse effects, but for Pipewire, it's actually developed by the original Devs of pulse effects - in fact the original pulse effects repo is now the easy effects repo, the old pulse effects hasn't actually been updated for an entire year now, so you might notice it working less and less well.

To me, Pipewire is the best option for audio on Linux at the moment, it combines the power and low latency of JACK with the ease of use, and multiple device capability of PulseAudio, it really is a great project and is pretty much rock solid at this point in time. It might also fix your issues with pulseeffects/EasyEffects not recognising your microphone.

Honestly, I still don't use flatpaks for specific things - namely OBS, as I have a Blackmagic capture card, and the flatpak version of OBS won't support it due to how the BMD driver is required to be installed. Sure it's good for a lot of things, but sometimes the other options are better for your purposes. I still use the AUR Tytan652 version.