There's a mod called Deep Mine ( https://mods.factorio.com/mod/DeepMine ) that works similarly, which uses hidden beacons with productivity modules to allow the mines to benefit from Mining Productivity research.
The problem with Equivalent Exchange is that the resources are generated through Assembly Machines. Which means that applying the exact same mechanic of productivity beacons to this mod will cause Assembly Machines to benefit from it for any product they're producing, which of course would throw balance completely out of whack. I would guess the only way to make it work for Equivalent Exchange is for the mod to use its own unique entities to craft ores.
I used Optera's Deep Mine mod's hidden beacon for a personal use mod to have K2 Matter Assemblers benefit from Mining Productivity (And removed said machine's ability to craft intermediate products in that mod) so I can tell first hand that the code would be very easy to implement if you were to create your own entities to create these raw materials.
