Maybe because Bethesda manager changes your plugin.txt or other.
Make a backup copy of it, even better, backup your Fallout4 folder in AppData where is the plugin.txt. To be sure backup also your Fallout4 saves folder in documents, where are the ini files and of course your saves.....and backup even your Vortex settings.
I don't know Vortex but I imagine it has an installation folder with the executables, settings, etc....backup its folder.
When you installed the mod from Bethesda site, created the mod files backup and uninstalled it from the Bethesda site, you have all the backups to revert your game status before the Bethesda hurricane
Just a suggestion, look at the Fallout 4 main folder, just to know if it installs a file or a folder in that directory, so you can easily delete or rename it when you've done to disable it. Usually when I want to deactivate something but I'm not sure if I can delete it, I rename it with four zeros in front. For example.....mod.txt. I rename it to 0000mod.txt and it's disabled.
If you want to be sure in a second time, order the files by date and you will know what are the last files and folders created without your knowledge.
So for whatever reason installing anything straight from bethesda break smy animation mods. What I actually ended up doing was downloading Animated mannequins and just adding in my own animations/poses. Actually it's a better solution than what I was initially looking for anyways.