Oh yeah, this is another aberration! The .45, in fact, is a pistol round. This is confirmed by the fact the Fallout 4 Submachine Gun (which is copied exactly from the real world Thompson) is chambered in .45, just like its real-life counterpart. For the record, a Submachine gun is an automatic weapon that fires pistol rounds while being bigger than a pistol. SMG's have their niche uses, but were really popular before people figured out that you needed to make intermediate rounds and invented the assault rifle. Anyway, the Submachine Gun looks and behaves a lot like its RL counterpart. The weird thing is, the Fallout 4 Combat Rifle is also chambered in .45, which if the behavior of the Submachine Gun is any indicator, is indeed designed for pistols (although there isn't a .45 pistol in the game). The FO4 Combat Rifle looks and behaves like a Battle Rifle, IE, a semi/automatic rifle using full-powered rifle rounds. It's pretty silly that these guns use the same ammo, but of course that decision was probably driven by not wanting too many different ammo types.
While it is unfortunate the Submachine Gun uses exactly the same ammo as the Combat Rifle, the notion of a .45 rifle round isn't so ludicrous within Fallout's sometimes semi-silly context. After all, .XX calibre alone doesn't contemplate length, which determines whether we're talking about pistol or rifle bullets. For instance, the .50 calibre has been made into pistol and rifle variants.
That said, .45 being 11.43mm, a long rifle variant
might have a bit of a kick. It'd likely exceed that of the Browning Automatic Rifle (7.92mm, and possibly an inspiration for the FO4 Combat Rifle) by a fair margin.
EDIT: It'd be less outlandish for an assault rifle designed to be used by power-armoured soldiers. Like the machinegun-like FO4 Assault Rifle, if that was the intent.