Apologies my experience is with video games. Useally creating seams and manually unwrapping is my go-to method because I can control exactly how an object is unwrapped(though no padding can cause issues with really low texture resolutions because islands will bleed into each other). Then i use Substance to create all the textures and export them into the desired configuration and format.

Though I assume your textures will be saved in a format that preserves the layers so the user can isolate the body paint and the decals if they need to change them (don’t have much experience with that pipeline).

Useally what I do for decals is have them as a separate material using an atlas texture (grayscale only for alpha mask so players can choose decal colors) if users need to modify it but as you mention you can only have one material.

Also I want to guess that is a diffuse map for a train, never have the patience to do 1 to 1 recreations of real life vehicles (people get really picky about detail)