In bdr001.nxonnx32.bea only one file has that problem.
Even if 10 archives would have that problem, it's very different than saying that you have to rename "thousand files".
In that case you will be prompted to rename only 10 files which is something that takes no time.
That's at least the first one it caught. Later it'll start to extract a ton of texture files (around 259 of them) and you'd have to rename all of them manually.
Tho you could get the XCI, extract the files and test it for yourself since sharing all of them here would be kinda, ya know, not legal lol
Still tho, you could make the script ask "Is there a . between the path?" and then make a folder out of it and "Is there a . at the end of the path?" then make it a file. Not sure what's so hard about this workaround when the Engine devs/Nintendo can't do stuff properly