I've not dug into the code side of modding since 0.13(?) but is it not possible to change the next_upgrade on say the vanilla electric furnace or the vanilla research labs rather on than the prototype for all types of electric furnace and all types of research lab? or is that what you're suggesting but in technical speak? That would mean your primitive and basic electric furnaces don't get upgraded by default to the beaconed ones but wouldn't their default upgrades be best served by the vanilla electric furnaces anyway rather than the beaconed ones?
Or are you already setting things in the electric furnace/research labs and then rather than building up from the correct prototype these other modders are building from the wrong place? The big furnace mod is compatible with built-in-beacons and has a larger than 3x3 electric furnace they might be building off the correct prototypes in which case it might be worth noting for other modders seeking compatibility what the best practice is.
(honestly I can live without mods when I come across conflicts but it's nice to have more options)