So in short the functionality in realistic reload where it actually saves the last ammo used on every specific gun breaks on inventory dump, so when doing dlc like the pitt and mother ship zeta; any save after starting them will still prevent you from auto-reloading on clip empty (sending in use ammo to the partial clip as well) but the previous stated functionality of the mod breaks. This could be a result of some hidden/invisible item in the users inventory that I have barely an inclination to the name of that gets dropped and lost when it leaves the players inventory; never to be seen again. So think of this as a "Help-me-look-for-weird-item-that-does-things-so-that-it-can-be-set-to-respawn-and-then-patched-and-fixed" thread and not a "lets-ignore-this-mod-and-reinvent-the-wheel" thread. but of course if I'm wrong in my theory and its something else and then we need to fix that, this thread is good for that too! so without further ado lets begin this session of the Think Tank!
edit: so after another 3 hours of digging through the nexus i found that the Gun Behavior Mod Merge helps rectify's the issue as it gives a MCM option to enable/disable Realistic Reload and as a result of doing so fixes ammo rememberance. So with that being said this could technically be considered Resolved, but only do to a Technicality.