Roughly speaking IRL breaking bonds between chemical compounds requires energy just like in your mod, but forming bonds releases energy. I dont know if its possible to implement this, but it would be really cool, if creating compounds would actually give you back some FE. For balancing reasons of course not as much as you put in, and the required power would probably need to be increased. For maximum efficiency you would therefore need an energy buffer.

It would also be possible to build an energy storage by deconstructing e.g. water into hydrogen and oxygen and at a later time reconstructing them into water again to reclaim a portion of energy (like hydrogen fuel cells do IRL).

Unfortunately the ammount of energy you need/get would have to be tied to the ammout of items in each operation (you get/need a specific ammount of FE for each Item you put in/got out). If the energy you get/need was fixed per operation, this could sadly be abused by deconstructing large molecules and then reconstructing them into many smaller ones, essentially creating energy from thin air.

Again, I dont know if this is feasable, but this conservation of energy would bring a huge chunk of realism to the mod.