Unfortunately, they'll actually be more restricted during the review process than they were before.
If, before the deal, they had decided they wanted to share characters or combine films or universes and both sides agreed, they'd just do it. The only thing preventing Tony Stark from showing up in Deadpool is that neither Fox, nor Marvel would have allowed it.
But there are laws that prevent companies in the process of a purchase from working together, and to avoid any appearance of impropriety they will probably want to avoid working together in any way.
BUT (and this is a key point) there's nothing preventing Marvel from filming scenes that include Reed Richards, Victor Von Doom, Ben Grimm etc. Anyone can film a scene with Reed Richards. It's only when it comes to publishing/distributing that film that Fox lawyers could step in with a 'cease and desist'.
So Marvel can film all the scenes they want now. They'd just be risking the money spent to film those scenes if they can't actually use them by the release date.