This is all with the Space Exploration mod:

The Portable Aneutronic Fusion Reactor has a couple of fuels for it of technology after it, the first is the He3-He3 plasma cell, which takes the same type of science packs as the Portable Aneutronic Fusion Reactor (the high one being deep space science pack 1), however in the tech tree it's parented to Deep space science pack 4, which puts it pretty firmly as (post?) end-game, rather than higher up in the tech tree with the Portable Aneutronic Fusion Reactor itself as it seems it should be at. The following fuel of D-He3 plasma cell is parented to the He3-He3 plasma cell so that also puts it well well past the endgame level of things. It seems like the only thing incorrect is the He3-He3 plasma cell tech is incorrectly parented to Deep Space science pack 4 when it shouldn't be (none of its science packs require anything near as end-game as that, and it's so far removed from the portable aneutronic fusion reactor so as to make it useless)..

Don't use the RTG mod with SE. SE has its own tiers of RTGs and a portable fusion reactor, although it works the same as the vanilla one.
I might make the SE fusion reactor use RFP fuel sometime in the future, but for now your best bet is probably using K2's portable reactors with RFP's replacement option.

I'm not using the Krastorio 2 mod, are its portable reactors available standalone?

Don't think so. It shouldn't be hard to make the SE reactor use RFP fuel though, so I might add it in the next update (whenever that'll be).