It appears that for some reason LTN is not registering the cargo and fluid capacity changes. I have attempted changing my fluid wagons to 200% and the build wagon tooltip shows 50k per wagon but LTN still believes that the value is 25k. There was also a forum thread on the LTN subforum where a different person was having the same problem with cargo wagons. (https://forums.factorio.com/viewtopic.php?f=214&t=72105) According to Optera's post in this thread I'm wondering if the problem is a mod load order problem. Namely Config Train Specs is modifying the wagon sizes after LTN has captured the wagon sizes.
Post by Optera » Mon Jul 01, 2019 5:49 am
LTN reads cargo size for every wagon every time a game is loaded.
The only way it would get incorrect size is if entity prototype would show incorrect values.