Windows 11 Pro.
How do I make the notehead size bigger for all noteheads in a flow without changing the staff size?
Use the Properties panel and Custom Scale.
Or you could edit the noteheads themselves in Library > Edit Noteheads.
Is there any way to preset the Custom Scale so I don’t have to do it manually?
No. Editing the noteheads themselves would be a better option if you want to always make them larger relative to the staff.