While it seems bizarre that a carrier would close flights at such an odd time, the agent's own words are just that.

Don't overthink this. The agent said that U2 closes at T-41 while it advertises and publishes on OP's specific ticket a deadline of T-40. It was the fact that the agent acknowledged T-41 which leads you to the issue.

I would file the claim, noting that you presented yourself prior to the deadline advertised, but that the agent told you this was not the local deadline. Accordingly you were improperly denied boarding and are due compensation.

Whether closing is automated is irrelevant to your claim.