That said, I've come to realize that it causes some very strange interactions on my phone and have stopped using it. I just wanted to give the heads up to other users.
Some specific examples:
I use Autoruns to control what apps are allowed to automatically run on my phone. After flashing CM7 and experimenting with the themes, Autoruns stopped working. Specifically, when started, it would no longer show all of the apps that have autostart privileges on the phone. Instead, it just showed a few entries for Android itself.
It didn't occur to me that the issue was because of the Theme Chooser. I thought it was just a Gingerbread and/or CM7 issue with Autostarts. But after speaking with the developer, he related to me that this was a known bug with applying a theme with the chooser. I switched back to "system" in the Theme Chooser and he was right: Autostarts returned to full functionality.
As a workaround, you can apply changes with Autostarts, then apply a theme afterwards. Your changes from Autostarts will stick, but if you need to make future changes you will need to revert back to the system theme temporarily.
The other major issue I was having was with WidgetLocker. WL would remember all my settings and sliders, but if I placed any 3rd party widgets onto my lockscreen, they would disappear on reboot. I tried all sorts of wipes / uninstalls / reinstalls, but the problem persisted. Frustrated, I again believed that this was because of Gingerbread and/or CM7. But as soon as I reverted my theme back to system in the Theme Chooser, this problem also went away completely.
I never contacted the WL devs, so I don't know if this second one is a recognized issue with interaction, but I can reliably induce the problem.
So I just wanted to pass this along. If you are using the Theme Chooser, consider reverting back to system if you are trying to investigate any weird problems. If two of the major apps that I use were affected, I'm sure some others are as well.
I'm not saying that the Theme Chooser has to be avoided: just that it should be considered as a variable when investigating buggy behavior.
(I am posting this outside the Nightlies thread as I'm not sure what other roms might be trying to user this theme chooser.)