There's a limit to what you can do with a bad model. Even paint won't hide defect.
As Chris van der Heide wrote in a comment, fading the GTW blue a lot would probably help to blend things together, including the paint mismatch near the lettering. In fact, since my blue coat of paint was relatively thick (because of the white primer), the fading wash gathered in this small crevices and made the patching process more obvious. Because of that, I didn't fade the color as much as I wanted to minimize this counterproductive side effect.
Rust was kept to minimum, according to prototype pictures, but I went overboard with the roof. My guess was that if the roof can steal the show, eyes will be more foregiving about the ghosting effect near the lettering.
All in all, the model isludicrous. A little bit better than before but still not great. It looks bad when compared to crude Roundhouse and Athearn BB kits. The car rides too high on its trucks. But still, I'm happy with the result. It was a good opportunity to try different technics and work with weathering powders. It was also a good opportunity to see how my kitbashing ability improved during the last months. I was effectively able to hack and saw this model in a few minutes. After an afternoon, everything was glued together. Sure, I didn't waste time puttying some seams because I felt it wasn't worth the extra time.