I'm having trouble replicating this. Were you using other mods which change the effects of qualities or add new qualities? I've come up with some code to better accommodate custom qualities but want to be sure it addresses the problem before publishing a new version.
This may be unrelated, but I'm also noticing that when these two mods are used together, the allowed_effects for beacons doesn't include "productivity" by the time my mod starts evaluating which values are possible in data-final-fixes.lua. So some power consumption values that are only possible with prod modules (e.g. +80% or +160% in vanilla) don't end up working correctly. You could update the allowed_effects for beacons in data-updates.lua (in addition to data-final-fixes.lua) to fix that. Alternatively, I could add your mod as a dependency so that it loads first.
Actually, I do have a mod that adds new qualities.
And I've confirmed the mod works properly and I am able to load a save when this https://mods.factorio.com/mod/Additional-Qualities mod is disabled.
As for that latter part, I'll do something on my side when I can but if you're going to do that alternative part, I think you should also include the other mods that enable putting in prod and qual modules into beacons. Since mine only does that one specific thing but the others also do the same thing and more, to prevent confusion. Just my thoughts.