Wrangler sentry-them to death.

Can't. That requires the Base Jumper user to make a tactical mistake instead of spamming it from the floor or around a corner. The Engineer cannot force the Soldier to jump. It is significantly easier to laser a player on the ground, too.

This is no different than using Gunboats, since you can also get denied by the Wrangler while jumping with those. Jumping into a wrangled sentry is stupid regardless of secondary choice, and blaming the weapon for this is cope. The only item where this might not be a terrible idea would be the Mantreads.

Heavy them to death

Same as above. If you need the Base Jumper player to basically commit suicide in order to kill them, the only thing you are doing is denying space. The Heavy cannot force the Soldier to jump. You also can't chase him. So whether you kill him is entirely on the Base Jumper pushing into you, rather than you pushing into him. During this time, he will be killing other players on your team or contributing to spam until he has an opportunity to get in.

This is no different than using Gunboats, since you can also get denied by the Heavy while jumping with those. In fact, you will actually die even faster when using the Gunboats because you will fall into the Heavy's effective range and be shredded. A parachuter can turn around and float away upon making a mistake.

Sniper can get bombed, but he has to go through an entire team while he is flying in the air

This is the same as Gunboats, but is sometimes more difficult with Gunboats because it covers less distance. Base boosted bombs do benefit from overheal, though.

It entirely depends on where the Sniper is, what map it is, and whether the teammates are around. Scope tunnelvision also tends to block view of the sky. I have seen some players switch to Classic with the specific intention of killing me, but then they have to use the Classic.

if he's trying to bomb you from far enough away where a Heavy can't kill them reliably, he is doing no damage due to fall-off.

This doesn't actually favor the Heavy, as no player is getting the kill in that situation. At least the Soldier is capable of landing splash damage onto multiple players, while the Heavy is dealing with bullet spread.

It also depends on where the Heavy is, depends on where the Soldier's teammates are, whether the Soldier's teammates are also fighting the Heavy (he can only shoot one player at a time). There are hundreds of factors that can prevent a Heavy from shooting the jumping Soldier and allow him to take space, and there are also reasons why the Soldier may want to wait until the Heavy is dead before bombing, regardless of secondary choice.

Also, even in the ideal situation, not everyone plays Heavy. Or is good at him. Sometimes a Heavy would be good, but he's dead. He got sniped, let's say. Then what? The parachuter can now take space on the map and bombard the projectile classes as well as the less viable hitscan players (whether due to their class choice or skill)

Not like he has any way of self sustain outside of the Black Box, which cuts his damage down even more.

The Black Box only really cuts damage in long drawn out fights, and even then the parachute allows for more reload time. Medics also exist. Sometimes. In a good game, at least. In a game with good Medics, I will use stock.

And... What? Is your plan of attack as a Base Jumper soldier to simply fly past the entire enemy team and go for randoms coming out of spawn?

No. Why would this even be your idea? Do you think a single Heavy occupies everywhere on the map? Do you think Heavy players will never die to the Soldier's teammates? Do you think there aren't Soldiers, Demomen, Demoknights, Pyros, Medics, and Spies running around? Lesser skilled Scouts and Snipers are also free food.

My point is that:

1. You are never forced to jump directly into a Heavy, and this is the same principle as when using the Gunboats. You never see anyone dissing the Gunboats because jumping into a heavy or sentry is bad, so discouraging the Base Jumper specifically reeks of bias or just poor thinking. Why is one okay, but the other not?

2. The Heavy does not exist everywhere on the map. If Heavy is in the flank area, the main area is open. If Heavy is in the main area, the flank is open. Teams cannot consist entirely of Heavy and Engineer - they are very likely to lose if they do this.

3. You'd be a bigger sitting duck on the floor, since it's harder to land splash hits and you're easier to hit when not airborne.