To use the inner holes as designed I’ve found it’s best to start with a thru tap (in 1/4”) and then move to a bottoming tap. The thru tap should only be turned through four turns or it will punch through and create an opening for gunk to get into the electrics. I apply a bit of rocol rtd during tapping which allow me to easily pick up the swarf with a rag.
I have a harmonic balancer puller that I use to remove the flywheels; the one I use is an older unit and is smaller than some of those commonly sold today. The bigger modern models don’t let the bolts get close enough together or let you easily use the 1/4” bolts.
Another thing is to apply penetrant to the thread a couple of days before, this helps a lot. The sleeve on the flywheel can corrode and bond with the crankshaft and the penetrant helps.
If I feel any resistance I back off straight away and use heat differential to help me out. I then choose to do the job early in the day as it gets pretty chilly in my workshop overnight and the whole mower is cold. Having put the puller in my deep freeze overnight I use my heat gun to warm the flywheel. The heat expands the flywheel relative to the crankshaft and the puller works more efficiently.
I haven’t broken a flywheel in a while, I’m much more cautious since early motors and spare parts got scarce.