The nuclear and fusion assemblers can't craft from the basic-crafting category (unsure if this is intentional or if basic-crafting is from SE) or the kiln category (added by SE). I don't know if there are other categories they should be in or if there are other machines with a similar compatibility issue, but I've not found any personally. It would be nice if this compatibility could be added in. Additionally, perhaps the fusion crafting machine could be allowed for space crafting or some other later-game SE crafting given its resource and research costs, although that's less important in my opinion.
You could make a PR for that otherwise I must say that 248k is very low on my priority list currently, since pretty much all of my dev time goes into EI.