Originally Posted by JeromeGrasdyke
This is because the fallback directory for the BI exe (version 1.4) is the Rome dataset. This should allow you to make Rome mods which incorporate BI features, although you will want to keep in mind that not all BI features will be available in the 1.3 exe.
That means that when you're making a mod this way, you're always starting from the Rome dataset, rather than the BI one. If you wanted to make a BI mod which leaves the original BI untouched you could write a little installer which made a copy of the BI directory, renamed it to 'minimod', then installed your extra changed files into it and added a program shortcut to the base directory called "Minimod" which starts rometw-bi.exe with '-mod:minimod' on the command line.
It may sound a little confusing at first, but I'm sure people will get the hang of it.