Pack Files that PFM has edited require "enable out-of-date mods" to be selected in Rome 2 and Attila's launchers in order to actually load. This is also the case with Pack Files created by Rome 2's assembly kit. I have not confirmed whether other assembly kits have this problem or whether other games have a problem with PFM's pack files. This may be a bug with the games' launchers and not PFM but I am documenting it regardless in case a solution can be found.
It is possible that they check the Pack file header number (PFH<x>) to be the latest the game is able to digest. PFM does not currently have a way to edit this number directly (I never got around to doing that and it never seemed that necessary). However, if you create a new pack file for a game, it will create it with the highest header number it knows the game can handle IIRC.</x>
Upon further inspection, there are no practical differences between a user-created mod that won't load and a workshop mod that will load apart from the lack of workshop metadata. Adding an image for the mod doesn't make it load without the "enable out-of-date mods" checkbox. Uploading the mod to the workshop does make the mod load without enabling the "enable out-of-date mods" checkbox. This is entirely an issue with the implementation of the Total War launcher and not with PFM or its created pack files.