There are inherent problems the .45 Colt has that the .44 mag. does not. Most (commercial) guns chambered in .45 Colt have over sized chambers (not a problem with Freedom Arms guns), with higher pressure loads the case swells, contracts and after just a few shots, work hardens to the point that the cases split. The commercial .44 mag., guns do not suffer from this problem. The .45 Colt is notorious for having tight throats, a detriment to real accuracy, again a trait not as common in the .44 Mag.
I have a fairly nice collection of handguns, and most of them are chambered in .45 Colt.
With the bullets/loads available today, the difference in the two loads .44/.45 is pretty much like beauty, it lies in the eye of the beholder.