Now that, as per Minecraft 1.7+, item/block IDs are the same across installations, it is possible to add mod entries to the InvTweaksTree file and re-use this file when changing to a different modpack.
Sadly this is a painful process and if you want to support all mods in a modpack you're gonna be busy for a while. Not to mention the file is going to be huge.

What I suggest is allowing other InvTweaksTree files to be included from the main file, so they can easily be made/distributed on a per-mod basis.
This would allow mod authors or community members to distribute their own InvTweaksTree files on a per-mod basis.
The end user/modpack author would only have to add a line like <include file="path/to/other/InvTweaksTree.txt"/> to the main InvTweaksTree file.
Of course, this would require allowing the same categories multiple times and would require merging 'em if duplicates are found.
Doing this would break the order of items in a category, although I don't think that order is still used anywhere since Minecraft 1.6 or so.
Pressing the sort key multiple times cycles through the different items in that category nowadays anyway.

I like this suggestion quite a bit as it means that InvTweaksTree getting blown away by an update won't destroy my additional stuff added for eg Pams Harvestcraft.

What if there were just a bunch of .tree files in a InvTweaks config folder that it merged before loading?