I am trying to use your mod instead of the Noxy's mod.

So I've disabled Noxy's, loaded the existing game with your mod and reasearched the both proper technologies. I've got messages about my trains replaced with MU versions.

Now inserters don't load MU locomotives with fuel, neither with coal, nor with nuclear fuel.
As soon as I remove one locomotive from the pair, the other one is replaced with a normal locomotive and starts being refuelled.

I am using over 90 mods, but I believe the collision could be with the "Train Skip Fulfilled Station" mod.

That's interesting. It might be an interaction with MUTC's fuel balancing logic. You can try disabling it by setting the "Ticks Between Fuel Balancing" value to 0. Then you will need one inserter on each locomotive as usual, but the mod won't make fuel appear and disappear in the locomotives by itself.

I just started a test game with just MUTC and Train Skip Fulfilled Station, and fuel inserting and balancing seems to work fine. Obviously, if the only stops with refueling available are always skipped because the conditions are fulfilled, it will never get a chance to refuel. Can you post your full mod list?

Thank you for the hint, now I get it. So it's not a bug.

Well, that was not obvious without reading detailed explanation =) Could you, please, add the info about fuel sharing into the technology description, for example?
From my side it looked really weird with one fuel inserter working, the other not working, Inventory sensor showing a locomotive with fuel that was never loaded into it, etc =)

On the other hand a two-headed train now contains only 5 of possible 6 Nuclear fuel (3 in the head loco, 2 in the tail)

I can certainly add it to the technology description. It's explained in the mod portal description why I included the feature, because otherwise the front locomotive would run out while the back still had plenty (even though they were both "supposed" to be doing work).

If you have inserters feeding both locomotives, they should still both fill up. If you're lazy like me and only insert into one of them, yes they don't both get completely full. It's a rounding error thing :)