Alaises in the git config file also give an error. You are forced to enter the full address to the repository.
Configuration:
Normal address: ssh://git@repo.com/repo.git
Alias address (using git config): repo:/repo.git
host repo
identityfile ~/.ssh/id_rsa
port 8090
user git
hostname repo.com
Error:
Unable to open connection:
Host does not existfatal: The remote end hung up unexpectedly

The workaround is to save sessions in PuTTY to use as aliases (as detailed on the Answers thread).

That will work, however not to bring up other Git clients, the norm is to have different options for authentication, those being PuTTy and Git Bash. By default SourceTree is configured to use Git Bash so I would expect it to use it for authentication as well. Maybe a feature request?