Not exactly sure of the timing (exact seconds), but it's real time based. If you dock at intermediate ports, the perishable will keep rotting away.

My best run was from New London to Manhattan - 4 system jumps - and only loosing 5 units of luxury food. The worst run was loosing 9, after a few trade lane interruptions and waiting for those stupid AI large transports at the jumpgates.

Luxury food loss between New Tokyo and Honshu - 1 system jump - was 2 units, a few times almost 3 (the 3rd one's health was down to a speck). With the loss, a better profit than with Luxury Goods in a 70 unit VHF.

A trick - if you find yourself approaching an intermediate base when your perishable cargo is damaged, you can dock there, and in the commodity exchange there sell one of the damaged units of cargo and buy it back. It will be restored to undamaged condition, although you won't get back any that you already lost. It's not really worth bothering to do except maybe for Alien Organisms if it's really far into the red, but an interesting little detail.