I have always felt that having a removable transformer upgrade was a very neat piece of code, but ultimately more dangerous and cumbersome than it is fun and useful.
Would it be possible to make the relatively few machines (5 of them if memory serves correct) into separate blocks?
Firstly, because there is no way to supply any of those 5 machines with higher than 2048 EU/packet, transformer upgrades that stack past 3 are not reasonable.
Therefore, you would only have to designate 3 sub-blocks for each of the 5 machines.
Their ID's could even sub-ID's and their textures would not need to change (unless you feel like a slight recolor is necessary).
p.s. I am not forgetting about the Induction Furnace .
That machine has an all together different power/work trade off mechanic than any of the other machines.