I think most people would disagree with you and want those artifacts in version control, based on all the feedback I got when this project launched without .vespene files. I was basically eaten alive :) But yeah I sort of agree with you - I don't want to learn some funky language to define builds, and that's why I tried to keep this language simple. You can 100% just use the GUI if you want.
You can make pgdumps of it for backup.
Partial backups may be tricky, but I don't know if I understand your use case for partial backups then. I thought it was around quickly restoring just projects - which imports help with, and not build history. But really it sounds like if you just want to clone a server, full DB backups are going to be fine for you.
On other topics:
I think what you've suggested has implied a couple of features, one is a UI feature for "copy project".
The YAML document you have shared is unfortunately not doing what you think, because of all the same things called "name" will clobber each other and the last ones win. This is because YAML is representing a dumb hash here, not a list. It's an easy mistake, and I'd consider it a flaw in the YAML spec, but it's there in JSON too if I recall correctly.
YAML does have a thing called "documents" where different structures are seperated by "---" and I think that's also a really good feature to add to the importer, where each document gets created. This would allow exactly what you want and I REALLY like this idea.
This would be an easy contribution for someone who might find it interesting to work on.
I'll file both of these ideas (copy button + multiple documents in import) on GitHub, i can't promise they are at the top of my stack of things to do, but they are good ideas.