I think the difference in the base is a real issue. The other thing is bullet diameter. If I recall, originally a 44/40 used a .427 bullet but it was so close the a 44 spl (.430) that now 44/40's use .429 0r .430.
Whether slugging a bore and sizing bullets makes any difference- I don't know.
IAE, the big problem with the 44/40 was that balloon case that couldn't take high pressures. I have asked A LOT OF FOLKS why a modern, solid web 44/40 case cannot be loaded up to NEAR 44 Magnum pressures IF USED IN A GUN THAT CAN HANDLE IT. In other words if you have a gun with frame and cylinder that takes a 44 magnum, if the thing is chambers for a 44/40 could not similar levels be obtained?
From what I found:
44/40 Base .471 Rim ,525
44 Mag Base .457 Rim .514
That means more metal around the cylinder wall on the 44 magnum so the 44/40 would have to be backed off some. Trouble is- the safety police keep having a fit.