You see, advtrains includes a "japanese" train. Usually when peoole talk japanese trains, it's either bullet trains, a.k.a. shinkansen, or Tokyo-area trains. You don't hear people talking about Gono Line Resort Services or the Kansai Main Line. The "japanese" train in your mod possibly refers to a Tokyo-area train.
In fact, it is painted like a Yamanote Line Class E231, Saikyo Line Class E233 and Yokohama Line Class E233. I do find the JT to be emulatimg the E233 due to its lack of "separated" headlights, a feature of earlier trains.
Spoiler
I ask: please fix the model or fix the textures. :P
You don't have to, the mod is yours, and I could point every single problem regarding graphics, like each subway car having exactly two sets of headlights and two sets of tailights or high-vis blue coloured beacons on the track, or tiny semaphore lights on a giant grey plate... It just kinda bothers me, but I could probably make my own texture "pack" of only two textures giving the JT its Resort Hybrid appearance.