First of all, gnome-builder is available in Standard Ubuntu repository for Ubuntu 16.04 Xenial Xerus. The answer was for 15.10 I assume.
$ apt-cache policy gnome-builder
gnome-builder:
Installed: (none)
Candidate: 3.18.1-2ubuntu1
Version table:
3.18.1-2ubuntu1 500
500 http://us.archive.ubuntu.com/ubuntu xenial/universe amd64 Packages
Secondly, using PPAs means you're using some custom distribution. You're no longer on Ubuntu's upgrade path. It's OK as long as you're able to tackle any issue rising from using these PPAs.
Specifically, Gnome3 Staging PPA will likely to break your GNOME installation very much. Other Gnome software might not work with the latest versions of gnome libraries and hence you'll be unable to install them. However, you can always use ppa-purge to return back to Ubuntu repository.
My personal experience with gnome3-staging PPA is very bad. I would not recommend not to use that PPA to anyone who is willing to stay on Stable path.
Quoting from PPA page directly,
=== WARNING ===
The packages here have been deemed not ready for general use, they have known
bugs and/or regressions, sometimes of a critical nature.
Mostly things should run smoothly but be prepared to use ppa-purge, when you encounter issues!
If they break your system, you get to keep both halves.