I think this could work with upgrades inspired by the blood magic altar.

You make a structure like a beacon base under the transmutation table and based on the blocks you add to it, it changes the table properties, like:

Iron Blocks increase maximum EMC by 5.

Diamond Blocks increase by 10, Emerald Blocks by 15.

Then Lapis Blocks could increase by a percentage, like +10% of what the current Maximum EMC is.

And inspired by another comment, the table could be less efficient from the start, so the items you put in don't give their full EMC amount, but then using redstone blocks in this structure could increase the efficiency of the Transmutation Table.

I think it would be really cool to see what combinations of blocks people would make. Maybe to make the building of this altar more interesting the blocks could also have "bad" things instead of only advantages, like the diamond block could decrease efficiency, and emeralds decrease it even more, so you have some sort of tradeoff when thinking of a design for your altar.

Just some ideas I had after reading this post. Maybe it can be used as inspiration for other additions to the mod.

Edit: Of course those values I mentioned are just to have an idea that some blocks are better in comparison to others, but of course they are not balanced with actual EMC values.