In theory it would be possible if you modified the installer to run the permissions stuff on upgrades, but to be safe with that you'd need to set all existing permissions (user groups, users, moderators) to Not Set.
I really wouldn't recommend it. It certainly wouldn't be "supported" if it went wrong.
Safest approach would be to do it manually, the Installer contains lines such as this:
The second parameter, e.g. 'view' sets up the "View media" permission. If a user currently has the XF 'viewNode' ermission ("View node") then they will be given permission to "View media". The last paramete denotes whether it should be applied based to a moderator's permissions as well as globally if a moderator has that permission, e.g.
If you have the "hardDeleteAnyPost" global permission, you will get the "cropAny" global permission. Because of the "true" at the end, it will loop through all moderators and if a moderator has the "hardDeleteAnyPost" permission, then they will also get the "cropAny" permission.
So you could go through that hefty list, and apply them manually.
Though, ultimately, it's mostly common sense and not always accurate as there are far too many assumptions that may not be appropriate for your board. I'd recommend Martok's approach.