1am or 1pm?

If it's 1pm, I'll take Millbrae BART over either any day - at least if headed to Intl G or T3 like I normally am. Driving into the car park at 1pm will have you walking into the Intl terminal at 1:13pm on a weekday or 1:18pm on a weekend.

On a weekday through the day, BART is almost always going to beat the long-term parking train. BART runs every 15 minutes and takes 4 minutes, so it's basically a worst case 19 minute trip (best case 4 minutes) from walking onto the platform. If the Airtrain is 5 minutes as stated, then it needs to be no more than a 14 minute trip to best that as a worst case, and even less to win on average. I've never timed it, but it seems to me it would be at least that long.

Coming from the south (as I am) you also save a few minutes driving time - although obviously from the north that's the opposite.

The catch with BART is that service outside of peak hours is far less frequent, and overnight non-existent. You do also run a bit of a risk from a service disruption perspective (eg, I flew in a day or two after the last big wind storm and they were still recovering. The SFO-Millbrae train I was planning to catch was cancelled which would have meant a 15 minute wait - although in the end I was able to go via San Bruno and it only added a few minutes to the trip). There was a time when Uber was only about $10-15 from the airport to Millbrae as a backup, but recently it seems to be closer to $30.

But if the timings work, it's hard to best it from a cost/timing perspective. Less than $40 for a weeks parking including round-trip travel (for one person) beats anything else hands-down!