Currently, circuits are bugged with the mod, as carbon is required for them (which is unfortunate, as carbon can only be produced after making green tech cards, requiring circuits). Additionally, a few different fluids overlap as in natural gas. Any plans to fix these in the foreseeable future?

That looks like it'd be quite a project to make work in a sensible way, not just a simple fix. I don't think I'd expect any official support at all. A third party mod to make everything work together would be quite possible, but someone's gotta come along who's interested and has the time and capability, and no guessing when that'll be; personally I've got enough other things on my plate already.

(At first blush the thing that concerns me is the mysterious energy crystal, and how it's main ingredient ties into the 248k oil recipes.)

I did some experimenting. Since the fork of Bob's Electronics that ATOM uses didn't change any prototype names, it assumes that any item named 'carbon' is from another Bob's mod and okay to use, at which point it doesn't get replaced by graphite.

Considering the overlaps with 248k's kerosene, the need for acidic water (back to the aforementioned kerosene), SE's methane (much more energetic, oops)... Well, I really wouldn't hold my breath on this one.

Sorry, I'm not making it happen. I don't have enough time anymore for new big things. If someone else wants to write compatibility code, feel free to PR it :-)

That's unfortunate but understandable. Good luck with everything else!