Pretty much all of the Train Simulator content developers (including DTG) do not have a problem with distributing FREE repaints of their product as long as the geometry files are left out. It forces the user to have or purchase the base product on which the repaint is based... which equates to another sale for the content developer. There has only been one content developer (that I can remember) that became a stickler for no repaints, and they have pretty much lost a fair share of that market due to their policies. But that was their business decision.
As for Jointed Rail, their EULA probably covers distribution of reskinned product. While the above process only involves new textures and scripts, the base textures are still the intellectual property of Jointed Rail. But you're doing the right thing by asking for permission and I applaud you for that.