I agree that driving or flying back from SD may not make much of a difference. There is always a chance of traffic or bad weather on the roads but there's an equal chance of traffic/delays at the airport. The problem with Franklin driving back (at least in Columbo's mind) is that it makes him seem suspicious, as it comes across (again, to Columbo) as less than concerned AND it gives Columbo reason to suspect that Franklin drove back not to save time, but to transport the body so as to dump it on his front lawn ("There he, there IT was..."). Columbo is suspicious because of the fact that Franklin shows no real emotion - his comment above, the opening of the mail and the driving back instead of flying back all point to him as a guy who seems rather cold and calculating rather than being upset about his partner of 15 years being murdered.
Flying to L.A. from San Diego, whatever the real world drawbacks may be, was a better option in the Columbo-verse. By dumping the body on his own lawn Ken was trying to reinforce the idea that the motive for the killing was due to Jim’s mafia research. As mentioned above, bringing police attention on his own home gave the already suspicious Columbo an opportunity to poke around. That’s when he noticed the opened mail, confirming his suspicions. Great episode.
Btw, how geeky am I to write: “a better option in the Columbo-verse”, lol