There are 2 separate issues here.

1. The OP had placed a bottle of wine in the care of a US employee that had assured him of safekeeping. Whether the employee was really empowered/allowed to do that or not, I don't know but if he/she agreed to do it, he/she did so representing US. Having it go missing later sounds like there's a black sheep ruining it for the flock.

2. Arriving 40 minutes (or 45 or 60) before departure to check bags is not unreasonable and since it is already posted, if you can't make it on time, that's your problem. If I remember correctly, checked bags need to go with the traveller as per TSA. It takes time for bags to be routed to the aircraft and in some airports, a LOT of time given the size (let's not bring up competence and efficiency issues). The carrier provides service within reason. Why should they scramble because you can't keep good time? C'mon guys, ding when it's appropriate not just because it's US. Every major carrier I've flown has this policy including the top tiers like SQ, VS and CX. Only difference would be some allows you check it clearly stating there's a good chance they won't fly with you while in our domestics won't allow it cos of regulation.