First, I'm happy that on the 4th upload attempt the beta finally worked 
There was 2nd reason why I made it this way. If the installer had already 'Rise of Mankind' folder included in the filepaths and the mod was installed to 'Beyond the sword\Mods\' folder, then when used uninstaller it deleted everything from Mods folder so I couldn't use this method as it would have deleted all the mods from that folder. Now, because you have to put 'Rise of Mankind' in the installation path, the uninstaller goes to correct place and only deletes my mod from the Mods folder ie. it works correctly.

There is Rise of Mankind in the installation path - look at the suggested installation path. However because the installer can't locate BtS installation folder, I used the same path that Firaxis used for installing Civ 4 and BtS. Of course you need to change the installation path to point to the correct folder and the path must include '\Mods\Rise of Mankind' in it or the mod won't work. I tried to make the installer look registry for BtS location but I couldn't find the correct entry so I left the installer use my manually defined path.It works but there is NO RoM folder to put it all into if you use a different area to put it in. I dont put it in the mods folder cause it overrides some of the maps. And the BUG mod overrides some of the python there.
There was 2nd reason why I made it this way. If the installer had already 'Rise of Mankind' folder included in the filepaths and the mod was installed to 'Beyond the sword\Mods\' folder, then when used uninstaller it deleted everything from Mods folder so I couldn't use this method as it would have deleted all the mods from that folder. Now, because you have to put 'Rise of Mankind' in the installation path, the uninstaller goes to correct place and only deletes my mod from the Mods folder ie. it works correctly.