Remove Site Owner from SharePoint Site sub-folders.

Hi
My company used to have a file server where we created folders for the different departments, IT, Finance etc. 

We created security groups and gave full access to these groups to their department folder and added all the staff from that department to the security group - giving them full access to all sub-folders in the department folder.

We then had the option to create sub-folders in the department folders for specific users, like if some of the team worked on a specific project, we could give only those users access to that project folder that was in their main department folder. We would remove inheritance from the parent folder and control access this way individually.

Since moving to SharePoint a few years ago, we set up SharePoint Sites, SharePoint-IT, SharePoint-Finance etc. and moved all data from the file server folders to these sites. All users now became Owners to their SharePoint Site, and so had access to all folders, even the ones they did not before, which was okay.

We would now like to start doing the same as what we did with the file server, create a folder in a departments' Site and remove access to all Site owners and then give individual users access to that sub-folder. From what I can see, and have read, Site Owners will always have access to all folders and inheritance cannot be broken or removed?

Is this still correct and is there any way to get past this?

How would I give access to a manager who might want to save a private department related document to the SharePoint Site and restrict access to the rest or some of their team. We do not want to use OneDrive for these situations, we would like to keep all department related documents and files in the relevant department Sites.