I found another method - seems to be much better.

I now have two Harmattan SDKs - let's name it SDK1 and SDK2.
A directory inside my host's home "MeeGo-workdir" is mounted as /home/user/MyDocs/workdir inside both SDK1 and SDK2.

I compile everything in SDK1 with "/opt/wunderw" prefix. Then I install it in SDK2 with make install, create .tgz archive from "/opt/wunderw" directory, uninstall program with make uninstall and finally delete "/opt/wunderw". This way contents of tgz file is only the freshly compiled program and only its files.

I will check how it behaves in real use. In short this method avoids creating multiple directories in /opt for each program and creating symlinks.