[Kube]

Most certainly the flywheel has been ground too much. You can overcome the interference as has been advised previously.
Once the flywheel is this far "gone" I search out one with more life.
Not a huge deal (probably not) but the plate will start out further away from the bearing. That equates to less usable life to the clutch assembly.
Plus, as the disc wears, how long until it's hitting the bolts again?
Flywheels are typically cheap as they cost so much to ship. If it were me, I'd search out a better one. Ask for the depth (accurate measurement) from the face to the bottom of the "pocket". You can then compare to what you have.
If the replacement needs to be ground (most likely) allow .015" - .025".