Did you ever get this resolved? I'm facing a similar issue...
Yep, iTMSTransporter doesn't support proxy username/password configuration, which makes it really difficult to use behind proxy.
It's been years and Apple didn't bother to add support for proxy authentication.
What you can do is set up another proxy "in the middle".
For example, configure CNTLM and point it to your company proxy using user's auth details.
Then point transporter to CNTLM, this time there's no auth required.
So then Transporter -- (no auth) --> CNTLM -- (username/pwd) --> Company Proxy
One thing, though, CNTLM only works with NTLM authentication and doesn't support Basic authentication.
So company proxy has to have NTLM authentication enabled for this setup to work.