I want to make system sizes in one flow different than system sizes in another. Is this possible yet? - I"m still trying to wrap my head around the concept of ‘flows’. Daniel’s Preces/Responses blog post nigh-on caused my brain to explode. 
Engraving options apply to the whole project.
Notation options apply to individual flows.
However you can easily change the staff size for a single flow. In Engrave mode, select something in the flow, right-click, and use the “Staff size” in the menu.
For that matter, you can set a different staff size on each system, if you so wish. In Engraving mode, add a System Break or a Frame Break (or select one that’s already there) and in the bottom panel under Format flick the Space Size switch and change the number.