I was able to get a step further.
For some reason it doesnt like an additional Task like described above. I don't understand why.
I ended up editing install-php-impl.cmd file in the same path \build\WordPress\WebRole\bin.
I have added this line at the end
%WINDIR%\system32\inetsrv\appcmd.exe add apppool /name:"VCPool" /managedRuntimeVersion:"v4.0" /managedPipelineMode:"Integrated"
And in fact, once deployed, it actually does that. :) It creates a new AppPool, which is fantastic.
Now I would like to change my second <Site> to this new created AppPool, but adding another line right after, doesn't help.
%WINDIR%\system32\inetsrv\appcmd.exe set app "WebRole_IN_0_VC/" /applicationPool:"VCPool"
It seems the second site is somehow not yet generated.
Is there a way to delay this execution by 30 seconds to make sure the second site is up and can be changed?