The problem is I thought Mozilla themselves have decided to go the way of Google.. that is releasing upgrade at a much faster clip and a lot of these errors are security / stability issues... I would say use in app upgrade when you have reviewed the release notes first
. Especially with mail clients, you don't get to control who emails you. If there is a security / stability issue that pertains to you.. it might be a good idea to do in app upgrade.
It is a bit unfortunate that Mozilla doesn't have apt source like Google does. I think it is a bit of a balance to wait for the repositories to upgrade every 6 months vs running gksu thunderbird when there is an update... in the end, you might get a pretty big bug and still result in breakage.
Besides you run as Superuser only
during the upgrade and revert after the upgrade (you have to anyways because your email settings don't get carried over). I have filed a bugzilla report on this.
Godwin: IMHO, a user should never
run a web browser or mail application as the superuser. As you have pointed out, running Thunderbird as superuser (via the gksudo prefix) means that you have no correlation with your mail obtained when running as a standard user. This is because the profiles for the user and superuser are in different directories, each with different permissions.
Apart from this practical difficulty, running these internet apps as superuser is making your system far more vulnerable and may well result in breakage.
To avoid problems, just ignore any "in app" upgrades and stick to upgrading via the normal repositories.