I think it's more of a YMMV situation depending on the check in agent.
On Tues my bag was 10lbs over on an upgrade to C flying JFK-LAX. I fully expected to pay a fee but figured it couldn't hurt to ask. I asked the agent if she'd waive the fee if I gave her a nice smile. Her response was she just did.
I certainly wouldn't expect a waived fee in the future but it never hurts to politely ask once.