Modular Machinery is really cool but it misses some crucial features. The first problem is that the controller has an orange texture so creating a multiblock with blocks that are not from Modular Machinery would result into very ugly multiblocks. My suggestion here is to add the ability to add new blocks with custom behaviours through JSON. For example creating a block with custom name, textures and functionnalities (Controller, Item Input, Fluid Output etc...).
It would be cool to be able to have different functionnalities for the same block. This would add the ability to have the Inputs and the Outputs on the same blocks or create one-block machines.
For the GUI, I think that you should choose a static place for each Input/Output. For example a fluid bar on the left for the Fluid Input, on the right of this fluid bar the Item Input and a bit further the Item Output. And if the machine doesn't need one of these Input or Output, the bar/slot doesn't appear.
I know that this functionnality is hard to implement but it's like the "ultimate" functionnality.

controller has an orange texture so creating a multiblock with blocks that are not from Modular Machinery would result into very ugly multiblocks

Lookup the changelog for the new version. Machines can have a color tag that recolors casings & derivatives of MM once the structure has been formed.

create one-block machines

This whole mod's concept is against this specific suggestion.

Ok thank you for your fast reply, I understand!