I've been reloading and shooting 44-40 for years. The 'bottleneck' has nothing to do with the difficulty of reloading it. In truth, the 'bottleneck' of 44-40 is so slight that you have to look closely to even notice it.
The thinness of the brass at the case mouth though does make 44-40 a bit fussy to reload. 44-40 brass tends to run only about .007 thick at the case mouth. 45 Colt tends to run around .012 thick at the case mouth. That thin case wall has everything to do with it being 'fussy' to reload. Improperly set up dies will often result in the case neck crumpling down below the bullet. But 44-40 is not difficult to reload once you have your dies adjusted properly.
But you do have to be a bit more carefull. That thin case mouth will not take much abuse, and if the case is not properly centered in the shell holder and one carelessly rams a case mouth into the base of the sizing die, the mouth will probably crumple and the case will be ruined. If one did the same thing with a 45 Colt or 44 Special, it would just shrug off the blow. So I always run my press a little bit slower when loading 44-40 vs 45 Colt or 44 Special. I want to be able to stop pushing on the handle if I feel resistance when the shell first contacts the sizing die. So running a little bit slower keeps me from ruining cases if they shift on the shell plate.
Another myth about the bottleneck of 44-40 is that it helps keep chambers cleaner than straight cases. This is also untrue. Again, it is the thinness of the brass at the neck that allows the case to expand better at relatively low pressures to seal the chamber and prevent blowby in a rifle. The thicker case of 45 Colt cannot do this as well at the same pressure. The 'bottleneck' shape has nothing to do with it, high pressure gas has no problems going around corners.
P.S. Perhaps the idea bottlenecks being difficult to load is the fact that no carbide sizing dies exist for bottleneck cases, so one must use case lube when loading them. Carbide dies can be purchased for any straight walled case, like 38 Sp. 44 Sp, or 45 Colt. Carbide dies allow one to size cases without lubing them. But Carbide dies would be hideously expensive to make for anything other than straight cases, so only standard steel dies exist for these cases. That means one must take the extra step of lubing cases, not really a big deal, but it is an extra step in the loading process.
It is true that revolver manufacturers have often gotten diameters wrong when chambering revolvers for 44-40. The original 19th Century specification for barrel groove diameter for 44-40 was .427, as opposed to .429 for 44 Russian, 44 Special, and 44 Magnum. In truth, old 44-40 guns often varied as much as .425-.430. Today, most manufacturers have standardized with .429 barrels for 44 Special/44 Magnum guns. These guns require .429 or .430 lead bullets to perform properly. It can be a problem seating .429 or .430 bullets in 44-40 cases, with those thin necks, it often leads to cases bulging down below the bullet. In addition, and more importantly, manufacturers have often gotten chamber throat diameter completely wrong for 44-40 revolvers, often having undersized chamber throats as small as .425 coupled with a .429 barrel. A prescription for innaccuracy. The first Vaqueros chambered for 44-40 suffered from this problem. Later, Ruger got it right with slightly larger chamber throats.
Lastly, the New Vaquero is not available in 44-40 because when Ruger did the math, they realized they could not guarantee that all SAAMI spec ammo would fit in the cylinder without the rims interfering with each other. 44-40 rims run around .525 in diameter, 45 Colt rims only run around .512 in diameter. It was not a problem in the larger Vaquero cylinder, but it became an issue in the smaller New Vaquero cylinder.