I learned a little of how to use ctm and its quite helpful, however theres a idea i have in my mind and it feels like its great for this mod but just cant do it.

Imagine if you could make a overlay texture dependent on a block, like Polished Andesite next to Calcite.
And to make the overlay a different block/model like piston.
This way i could make textures like random style ctm but more defined where i want the randomness to be.
The texture will depend on Polished Andesite of course, and would have the ctm property file have a field like "replaceWith" to set the different piston texture :D

However i understand if a block model is to much, like if it were to change to a flower pot model xD But would still be amazingly powerful nonetheless.

I do not understand what you are requesting. The connectBlock property of method=overlay allows you to overlay different textures depending on what block is adjacent to the origin block.