If you plan to use the same loads in both handgun and rifle platforms, and provided both types of arms are made using modern materials and methods, and assuming modern solid-head brass (remember. the .45 Colt started back in the balloon-head era), then I can't see any obvious difficulties loading the .45 Colt up to the same ballistic and pressure levels as a .44 Magnum. The .45 Colt actually has slightly more case volume than the .44 Magnum (41.6 vs. 37.9 grains H2O), and there are plenty of modern firearms that will shrug off higher pressure .45 loadings.
However I would personally follow this road with an additional degree of caution. As another poster recently implied during a 30-30 thread, I'm evidently a scaredy cat -- so be it! Both when originally introduced and officially today, the .45 Colt has a designed pressure ceiling of less than half the .44 Magnum's, 14K vs. 36K psi. Because the .45 Colt is strongly linked with the 19th-Century 'cowboy' arsenal, I would be concerned about mixing a high-pressure loadings with arms (especially revolvers) that are unable to safely handle higher, magnum-level pressures. I have an old Lyman loading manual from 1978 with a separate section for .45 Colt loads marked "for Ruger and TC Contender only".
If I was to choose this route, I think one of my precautions would be using .45 Colt brass headstamped either +P (rare stuff) or cut-down .454 Casull cases. Or perhaps loading the hotter stuff in nickel-plated cases and keeping them in clearly-labeled ammo boxes of a different color from any lighter stuff.
Mind you, I'm not so much talking here about getting your own ammo mixed up. I believe as a community we have to consider what might happen if someone else tried shooting a box of our handloads unaware -- in my case, I'm thinking about the possibility of my departing this world ahead of my wife, and my shooting stuff getting into the food chain posthumously.
I don't actually own anything right now chambered in .45 Colt, but I do own and handload for a 1911 and a Webley MkVI revolver that will both chamber the same .45 ACP cartridges. Since the Webley wasn't engineered to handle standard .45 ACP pressure levels, I use it with reduced-pressure .45 Auto Rim ammo exclusively to prevent any potential for mix-ups. I have a similar problem with .38 ACP (Astra M400) and .38 Super +P (another 1911) -- I handle that by loading for both using the lower ACP pressure levels.
Back to the original question: I think I would be inclined to go the .44 Magnum route for reasons of simplicity. It isn't backward compatible with .44 S&W, Russian or Special in the sense that you could accidentally fit the hot stuff in any of the older, weaker platforms. The Magnum's performance in carbine-length barrels is well-documented. The larger diameter rim on the .44 Magnum case would provide a theoretical extraction advantage over the skimpy rim on the .45 in lever action rifles, though whether that is ever a real world advantage I cannot attest.
This is my long-winded way of rationalizing the addition of some new irons for your arsenal.
FWIW, my .44 handguns are a Ruger Super Blackhawk and TC Encore with an 8" barrel, and their carbine companions are a bolt-action 77/44 and a Martini-Henry conversion.