Thats actually actually quite what I already did
http://omegatron.net/photos
Basically what I did was make a dumbed down index.php called say test.php and place the dumbed down code into a function I named. I could then return an array with header footer values and in my code simply call the require that file in my application and can load the vb header footer.
Likewise yes you have to softlink or place a modified copy of config.php in your other directory.
Definately note a user friendly as earlier versions and I think the vb5 sales will be reflected as a result.