rsync appears to work fine but, as you experienced too, it seems to think that certain files have no permissions set. On another web site I found this explanation (not sure if this applies but could be the issue):
Your problem stems from the fact that the Unix permissions on that [Windows] directory really are 0. All of the access information is stored in separate ACLs, which rsync does not copy. Thus, it sets the permissions on the remote copy to 0.
(Rsync on Windows: wrong permissions for created directories - Stack Overflow)
Maybe something like --no-perms --no-owner --no-group should be passed to rsync since permissions really don’t matter in this case.
The RemoteBuildTool seems to work for me since I see files being compiled.