As a practical matter, nobody's going to haul double stacks to Tj, on the trolley tracks or otherwise, so a height restriction due to 21' wire is mostly irrelevant. Port of SD doesn't do much intermodal anyway, and what little comes into town on BNSF is offloaded there and sent on its way as a truck. Extra clearance might have been useful for autoracks, but Toyota found some other way to haul their Tacomas out - if they're even still operating in the Tijuana area. If you look at Google satellite pics, you'll mostly see loose-car consists on the SDIY and its Mexican connection, especially tank and hopper cars.

21' is certainly high enough for Bombardier double-deck commuter cars. Coaster has to operate under the trolley wire to get into its storage tracks in SD.