Composer default paths settings tuning

While testing composer based setups got some malfunction. The whole story has came from "what if webroot is different than project root" as it was with my similar v1.6 projects.
Something like this:
```
\-- webapp
   \-- config
   \-- cache
   \-- database
   \-- vendor
   \-- webroot
      \-- extensions
      \-- files
      \-- theme
```
Didn't worked at all, so I had to adjust some settings.
Tested with standard and composer based custom setup like above.
I'm trying to test with a composer based plain setup, where webroot is same as project root.
Note: nut can't run with this setup as above 'cause it loads standard bootstrap anyway with default paths so it should have some fine tuning. _Fingers cross... please Trevis..._