I've thought about this a lot, because money is a complicated thing, especially when people are involved.
I think it makes the most sense for revenue splits to work a lot like how bundles work. If you've never organized or been in a bundle, all of the people involved have to approve the percentages / split for the bundle to go live. Once everyone has approved a bundle it cannot be cancelled or modified, but obviously for a project it would make sense for it to be changeable.
So, for a project with a revenue split to go live, everyone involved would have to approve it. And if the split was ever going to change, or a new person is being added to the project, or someone wants to delist the project, everyone would have to approve a new form. In order to prevent angry people from spamming split changes, there would probably be a limit to how often changes can be suggested by individuals, maybe once a month.
There maybe would be a setting [that contributors have to approve / consent to] that would allow some contributors to be considered "core", and others to be considered minor contributors. The only difference would probably be that minor contributors wouldn't have a say in whether or not a project can be delisted.
I think what I'm imagining is basically as good as it gets; itch.io moderation doesn't have to get involved, and while people might regret things they approved later, ultimately nothing is perfect. For larger projects [6+ people], it maybe would make sense to have a voting system instead, because if a single person in a thirteen person team is always rejecting changes because they're trolling or pissy, that would be a huge issue. And the difference between core and minor contributors would probably be relevant here as well.
Not sure about the tax problems you're discussing. I've never been at risk while participating in a bundle because someone else in the bundle didn't do their taxes properly, and I imagine things would work the same here. I think the whole point of revenue sharing is that nobody wants to be an accountant responsible for paying other people, and that they want the money to be split before it even reaches them. But I'm not a legal expert.
Your comment about someone selling the item on another website; I already sell all of my albums on both itch.io and Bandcamp. There is nothing stopping me from selling my music for less money on Bandcamp, and vice versa. It might be against the ToS of itch.io or Bandcamp to do such a thing, I'm not sure, but the point I'm making is that this can basically already be done. I think it falls outside of the purview of itch.io's responsibility, and it ultimately would just be a massive dick move if an individual developer sold an exe on their own website to bypass a revnue split. That's something the devs would have to hash out between eachother.
And finally, your point about who owns a project; there would clearly have to be shared project pages or something. Regardless of who initiates the creation of the project page, when everyone approves said page it would probably not be "owned" by any individual member of the team, and people would have to go through the aforementioned approvals processes to make changes. Maybe, when the project is first being created, everyone can approve a single person owning the project, which would allow them to make a lot of changes unilaterally, which would make a lot of sense for projects where one person did 90% of the work and everyone else just contributed a few assets.
Obviously none of what I'm suggesting is perfect, and a lot of it would be really annoying, but that's just how money is, and even collaborative projects with shared ownership in general; they're the kinds of things that can destroy relationships.
It would be complicated for itch.io to sort out how it works, but if they can make bundles work legally, I'm sure it would only be marginally more complicated to have shared projects.
EDIT: I forgot to mention this earlier, but I recall hearing that DriveThruRPG has revenue sharing, so it has been done before.