Custom battles from RTW mod folder with BI.exe

Was wondering if anyone could explain to me in words of one syllable if it is possible to have a mod-folder for RTW 1.5 that will play custom battles when using both the RTW and BI exe's - I've seen that there is a known issue on getting custom battles to run with the BI.exe, see here:
https://forums.totalwar.org/vb/showthread.php?t=55119
I'm not 100% sure I understand solution to that as it seemed to be using BI base folder but with RTW faction names - so what is different then from using RTW base folder? :dizzy2:

also would fixing it so BI.exe runs custom battles mean RTW.exe won't?