Although I have not done metal ones that way, only wood I have machined features into the rims of some similar sized cast iron ones on a 6″ rotary table.
You need to watch out for backlash in the gears so adjust as much of that out as you can and lightly nip up the table locks to give some drag and then proceed with light cuts other wise you will get a juddering cut. The milled finish is unlikely to be as good as a turned one so after doing the best you can by milling make an arbour so the flywheel can be spun slowly by the mill while you used some emery on the rim and sides.
Drill and ream the bore first then move sideways to do the edge without removing the flywheel from the R/T to ensure you keep things true and concentric.