why is the 45 colt shell holder different than the 38-40 or 44-40?
Because the rims are shaped differently. The rim of a 45 Colt is only around .510 in diameter, the rims of 44-40 and 38-40 run around .520 in diameter. Shell holders have an undercut on them to grip the rim of the shell. The undercut has to be loose enough to allow the shell to be inserted and removed easily, but it has to grip the rim securely enough to pull it down out of the sizing die, which usually requires considerable effort. Sizing dies often are tight enough that it requires considerable force to shove a fired shell into them. It also requires considerable force to retract the shell again. You don't want the shell slipping out of the holder and leaving it stuck in the sizing die, which is what will happen if the undercut does not grip the rim properly. 44-40 and 38-40 have the exact same rim shape, so they can use the same shell holder. Believe it or not, 45ACP and 30-06 have the same rim shape, so they can usually use the same shell holder too. I just bought a 303 British shell holder and it turns out it will work for 30-40 Krag too.
Now having said all that, I believe Dillon's shell plate for 45 Colt will also work for 44-40. I don't know that for a fact, I believe I recall seeing it though. I'm sure somebody will correct me if I'm wrong.