Hi Juli--
You can only define which fields sync between Marketo and SFDC and the instance level, meaning you cannot set different sync settings between workspaces. It IS possible to unsync fields though, if you feel like 400 is too many and it's slowing down your system performance. You can hide the fields from the Marketo sync user in SFDC, and hide them in the admin setting of Marketo. If you want to be extra thorough, you can create a support ticket with Marketo to have them officially removed.
As for the second part of your question, when you say "sync across," are you talking about lead records, or fields? It's hard to answer accurately without knowing more about your lead partition settings. It is possible to set up different lead lifecycles within each workspace to individually control when MQL leads are synced to SFDC. (It's a bit more complicated if you have lead partitions that are visible in more than one workspace. Leads in a shared partition would qualify for syncing in more than one workspace.)
That's a bit of a complicated answer. Hope it helps!
Kate