Taking out a permit to replace a toilet may be required but is a little fanatical.
But the flange should have been replaced, or at least a spanner flange used under the old flange.
If the toilet bowl isn’t bolted directly to the flange, the two can move relative too each other. This will leak.
And I never caulk around a toilet bowl at the floor. This makes removing the toilet later hard to do, eventually mildews and makes the job look bad, and hides any leaks that do develop until they’re bad enough to damage the ceiling below or rot out the bathroom floor.