I completely see what you mean regards the energy available. Hodgdon list loads which give 200gr@1000-1100fps at under 13ksi, in a modern rifle (such as the ones which are chambered in 44 mag also) with brass that can handle it there is no reason it couldn’t make 1000 ft-lbs. This of course is beyond book levels and is completely at the owners risk but is no different to 45 Colt +p or even loading modern 8x57 rifles to CIP levels (56ksi) rather than SAAMI levels (35ksi).
I looked out the old Ken Waters 'Handloader Magazine' article on the 44-40. The original BP and early smokeless loads in 'balloon head' form cases produced 10-12,000 psi for around 1,300 fps with a 200gn bullet in a 24-inch barrel Winchester M1873, M1892 or Marlin 94. Waters found that any load that exceeded those MVs / pressures in this type of case saw such massive case-body expansion that the case was scrap. For starters with the body expanded almost to the edge of the rim, it was impossible to fit a fired case into the press shellholder.
The later (now normal form) case with a solid case-head is much stronger, but is still a very weak case compared to that of other designs. The special Winchester High Velocity (WHV) load I mentioned previously for 1892/1894 or later type rifles actually produced a lower MV than my memory said, some 1,595 fps with a 200gn JSP, which Messrs Whelen and Mattern estimated produced around 20-21,000 psi pressure.
Waters found that even with today's brass and powders, MVs equivalent to the WHV is as much as the cartridge will happily accept, in fact is the absolute maximum, and with some combinations a bit too high. Cases loaded to that performance level saw excessive expansion in two Winchester 92s used for testing - a rifle and 20-inch barrel carbine model - and depending on the make of die tended to be over-sized. Result, very short case life, in particular a sharp ridge in the upper case-walls that very quickly developed into a separation in two, maximum three firings and sizings.
One cannot use the 44 Remington Magnum as a guide in this case. Unlike many older cartridges with restricted maximum pressures and loads such as the 6.5X55mm which are dictated by vintage rifle action strengths, in this model it is the case not the firearm that is the weakest link. The 44 Rem Mag is in a completely different pressure class level loaded to 40,000 psi in factory ammunition and its cases are designed to safely accept these pressures. The 44-40 is obviously at its limit at around half that. (Having loaded both cartridges for leverguns many years back, I know very well how light the 44-40 case is compared to the similar size 44 Magnum, and how thin its wall are. Starline cases picked up large mouth indentations as they bounced off the chamber and action edges in being ejected from a repro M1892 Winchester.)
Waters' rifle loads are peppered with warnings such as 'MAXIMUM load - CAUTION', and 'DANGER - do NOT use'. It appears that around 1,650 fps is just available with careful loading, so whilst the 1,000 ft/lb ME performance level isn't impossible, it is at the top end of the available performance range and requires both very careful load development and great care in inspecting cases and being willing to scrap them after little use.
Incidentally, I'm puzzled as to why people are referring to 0.428" JSPs as 'Section 5'. The only bullets still in this category are those that only have pistol applications. Not only is the 44-40 originally a rifle cartridge, but under the status quo ante which we have now returned to, the pre-Dunblane law, those calibres / cartridges such as 357 and 44 Magnum which are primarily handgun numbers but with a secondary rifle use were treated as being in the latter category.