This idea that the .41 shoots flatter than either of the other two enough so that it's an advantage is greatly overblown, if not just wishful thinking. Data I have for a 210gr .41 Gold Dot and a 240gr .44 Gold Dot has a very slightly higher BC for the .41 but higher velocity for the .44, both using the same powder and the trajectory is nearly the same, slightly in favor of the .44. The Speer 260gr .45 bullet has the same BC as the .41 so expect that to be a wash as well.
In use, for the handloader, the .41 is probably a better choice as a deer cartridge, just because it's milder and deer don't take much killing. However, in the Hunter model, the .44 is heavy enough and I wouldn't want the weight of the .41 when I could have a much more capable .44 or .45 in a slightly lighter package. For the handloader, there is no ballistic difference between the .44Mag and .45Colt. Both are capable of bullets the same weight, at similar velocity and similarly sized game. Both are a step up from the .41 in that regard. People have this idea that the .45 is a milder cartridge and that is simply not true. Either can be handloaded to duplicate one another. I lean towards the .44's for the simple reason that Ruger .45's often suffer from chamber/throat dimension issues.