If your difference is based on the user's role in certain Publications, I would first consider adjusting authorization in terms of rights, groups, and maybe permissions.
Otherwise yes, you could have Publication-specific Workflow Processes by unchecking the Publication setting for sharing workflows. See my post on Bundle Workflow for SDL Tridion 2013 (most of the details still apply) for this setting:
You could then localize Schemas to set different workflows per item across the BluePrint.
Alternatively, you could consider including Publication-specific logic in your Workflow Process Definition, but that seems harder to maintain to me.
I'm sure there are other solutions depending on your requirements. I'd just recommend confirming how the workflow process differs by group, content, and Publication to balance maintainability and flexibility.
Update: for scenarios where content creators should be able to influence the process of items in other publications, maybe consider Bundle (and/or item) Metadata to let the content creator adjust how the items are reviewed. This could influence a single workflow process or maybe start new ones, maybe?
Alternatively, you could have different workflow processes to let a certain process complete before starting the editing and publishing process.
I'm not sure, though, on making the list of Publications that allow editing and publishing changeable at any time. I'll let others answer; it could help if you add more details on how or when content creators would change these settings.