Sounds like this agent jumped the gun. Usually they'll communicate and offer coach on the earlier flight, and let it be the customer's call.

As for the Y --> F, CO will always do that. I know you are (were) a UA flyer, and unlike UA, where you can tell them to please waitlist me for F/C, and only clear me if you can clear me in F/C, CO will not do that. CO will always book you in your purchased class of service, then waitlist you for an upgrade. So, if you're trying to standby, don't clear til 30 minutes out, THEN you can request an upgrade to F, the likelihood of having F is near 0.