Because the smokeless pushes the bullet from the case into the throat and then starts to build its real pressure. From the point of ignition until the bullet plugs up the hole there is a gas leak, which tears up the bullet. Black powder is like a big hammer blow to the bullet, and it is so fast the bullet (and case) swells up and seal the chamber before the bullet moves much at all. The bullet is already filling the chamber and throat by the time it gets there.
Of course I can't actually see this happening but based on results and lots of experimenting this seems to be the case. I routinely demonstrate this effect by shooting bore diameter paper patch bullets in my 45-70. The wrapped bullet is smaller than the BORE - it just sits in there and will slide down the whole barrel if you want. Fired with black powder, that bullet instantly seals and shoots very well. Now we all know what happens if a smokeless load has a bullet even .001" smaller than the GROOVE size. It leads the bore and doesn't shoot accurately.
Pistol caliber lever guns are a special case when it comes to making good accurate ammo for them. We are limited by the action to how long a round can be, and what shape the bullet can be. But they are chambered typically with no real throat, just a taper from the mouth of the case into the bore. A funnel. If we load ammo with the bullet sticking out enough to engage the rifling, we will usually end up with ammo too long to feed through the action. So we must contend with the jump. In some rifles this is a real problem, in others it's no big deal. But the more we do to stop gas leaking during that jump the better our ammo will perform. If this involves granular filler, slower progressive burning powder, paper patching, black powder, or whatever else that is fine. The goal is the same. Get that bullet into the barrel pointed in the right direction with a minimum of damage. Once that has been achieved it will fly well.
I'll refer to my B92 again, since it has the opposite issue from the Marlin 45 Colt. The chamber on that rifle is exceptionally tight. A sizing die just barely changes a fired case, and a .359" bullet is tight in a fired case. But the throat is really long. (a cone 5 deg/side from .380" down to bore size) so any normal pistol type bullet has a long way to go to hit rifling. That rifle absolutely refuses to shoot with smokeless powder with any ammo loaded short enough to cycle through the action. But load it with rifle bullets, like the RCBS 35-200-FN seated to touch the rifling and it is a laser beam. Loaded with paper patched bullets to engrave the rifling and it's the same way. So I have a choice - if I want to use the magazine I load it with black powder and 158gr. pistol bullets (#358250 works wonderfully) and shoot accurately. Or I load it with rifle type bullets and smokeless and single load it. Thankfully on a '92 that is easy. Now with the Marlin and its big chamber, things are a lot easier. It will shoot exceptionally well with ammo loaded to function through the magazine, as long as the bullets are big enough. Those bottleneck 45 Colt cartridges might look odd, but they shoot wonderfully and feed slick. That 290gr. Ranch Dog bullet (.455") is designed just for this application, and the nose fills the throat when seated to the right length. All is good and the rifle is problem free.
This is getting long, but I hope it helps to clarify my thinking and helps to get these rifles shooting well. I know many people have trouble getting their pistol caliber rifle to shoot very well, or just accept that 4 MOA is all it is going to do. I wouldn't accept that and have learned ways to make them work. They are sure a lot of fun once you figure out how to make them sing!
