EDIT: Look at arizona480's post from March 21, 2009 - 7:24am on this thread here
https://portableapps.com/node/11309 and you have your solution!
I have a problem it seems many have had over the years, which is to use FF/TB Portable as the main and default programs instead of the local versions.
I understand there are problems where paths are being created in Documents and Settings instead of the PortableThunderbird folder and the start menu buttons point to blank versions of the programs.
There have been some answers suggesting how people could work around these problems, often just guessing and saying that it worked for them but then it didn't work for other people.
In the world of computer nothing is impossible and especially not if you know a bit about it.
Other people have just time and time again commented that one shouldn't aspire to making Portable your default, but that isn't helpful, seeing as the reason for asking was to find a way of doing it.
I understand that Mozilla wouldn't be too happy if everyone suddenly started using their program in a portable version that they haven't made, and so I understand that PortableApps must be careful in what it can and can't say about this issue, but nevertheless I think it would be safe to provide people with the choice.