Please star this issue:
I have to warn you, however, what you are doing (forwarding all traffic through a proxy) is dangerous. Google has some sort of attack detection and prevention system that recognizes malicious traffic patterns and blocks out access from suspect IP addresses. Because all of your traffic will be coming from a single IP address, if an attacker trips this mechanism, Google will block _all_ of your traffic.
This defensive system is totally undocumented, but it does exist - a couple years ago, this resulted in my website being shut down because I was proxying all traffic through CloudFlare. After about half a day of downtime, Google and CF got together and whitelisted the appropriate IP addresses. Running your own private proxy means this is failure case is less likely to happen, but it also means that if it does happen, you alone will have to work through Google's support tiers find someone who understands the issue.
I also run a whitelabeled system with hundreds of domains. The verification system is a huge PITA, especially because verification is tied to google *user accounts* and not the application project (that's right - the GAE "custom domains" panel looks totally different depending on who you are logged in as). However, there is an API for it:
I haven't tried it yet, but if you do, please report back.
Jeff