I've had all three. Bass drum mounted toms, stand mounted toms and now a single tom in a snare stand. If 2-up over the bass drum, mounting a tom to each cymbal stand is just obnoxious. At least one cymbal is going to be too big to position properly over a tom, so it's a constant battle. If toms are in the offset position, then a BD mounted tree for one and cymbal stand for the other is 10x more obnoxious, if you ever set up on an uneven stage. if 1-up, a BD mounted tom tree rarely allows proper positioning. In general, the setups that have given me the most trouble have been toms off cymbal stands. If I did that, then the cymbal was a splash or small crash. That way, it wasn't much different than a tom stand with a cymbal clamped on.
BD mounted tom trees aren't necessarily easier, and don't save any time if the stage is uneven. Setting up drums is just a pain. I personally prefer the independence of moving everything separately, so I can adjust as required. Looks better, doesn't look better, tom in snare stand is a hipster thing, it's cool if, isn't cool if...none of that matters, when I'm trying to setup and tear down in a flash. It's never mattered much if my FTs are on uneven ground. I have three legs to adjust. It's driven me nuts when my BD has been uneven and I'm trying to get it to sit right, but then my toms are way too far/close, one high, one low. If you're using a BD mounted stand then you just have to deal with it. This is where I give Pearl's "plumbing" mounts a huge nod. It doesn't matter how far off things go, you have a foot and a half of adjustments in each direction to get things right. If toms are on their own stand and not Pearl plumbing mounts, you have additional options. With a 1-up setup, if the tom is on a snare stand and uneven, happiness it's a wing nut away.
There's literally no one right answer, but there are tons on cool/not cool opinions.