~Very~ nice find on that site...
That is very interesting that the name on the stern is offset like that. There is an IJN regulation for that somewhere, I'm sure. At the end of the war, they did destroy a lot of records, trying to maintain "secrecy" - hence, us not being able to find documentation sometimes... and I would imagine, any "mistakes" we see in the kana & kanji would probably be a location that was somehow damaged, and took the paint off. I have never looked to see where a grid on a 3D ship model in SH4 shows on the stern... I'll have to go look now!
As for the implementation in FotRSU, we're dealing with a mod (FotRS) that the AOTD team worked on, with AOTD_MadMax as the team leader. As such, I'm sure he had modders that came and went, and probably ended up doing a lot of the work himself, though I do know that Rhonen (sic) was very active in the shipbuilding end of things, and they also borrowed mods from other sources. In the end though, real life dealt AOTD_MadMax several strong blows, such as loss of his job (more than once) and medical issues, so some of the things that they planned for the mod, and had partially implemented, were not completed...