I'm envisioning including something like this:

{
"y": 2,
"elements": "modularmachinery:blockinputbus",
"appearance": "charset:barrel"
}

And then, when the structure was recognized by the controller block, it would re-texture the casing elements of the block at (0,2,0) to resemble the barrel block from Charset. IMO, this would be much more useful and versatile for making these structures fit into pack aesthetics than just recoloring the blocks.

Along with the similiar suggestions that require hijacking the rendering pipeline of a world: No. This brings way too many problems and is highly unstable. I'd rather refrain from that.