Looks like I'll be dropping the BSA in the next version/Update.
This is common for mods that have bsa and esm and have esp that do not touch worldspace or place objects in worldspace.
Since the Arsenal comes a esm, and the leveledlist can get merged with bash. This will prevent the bsa from loading correctly because the LL esp itself does not make any changes to world space and ends up getting merged in bash patch.
While the store does because it make changes to worldspace which allow the bsa to load correctly.
So renaming the bsa to Bash Patched - The Arsenal.bsa should fix the problem if just using the esm and the LL.esp..