Yes, Covid has made us nervous.
@baymom1 Brown’s definitely far away, but also take into consideration that for many West Coast students (and especially for engineering/CS students b/c of Silicon Valley) they will likely come back home/close-by due to the plethora of job opportunities and a desire to be close to their family. I myself am definitely not opposed to coming back to the West Coast, but wanted the experience of living in another part of the US that’s different from mine before coming back here. I wanted a change of pace, and definitely what @bluebayou mentions in his earlier comment. 
Regarding COVID, there’s no way to know for certain how the situation will change over the coming months/years and at most of the colleges listed so far (Vanderbilt, UC Irvine, USC;) your son will likely have to live on-campus. In Brown’s case, they’re constantly assessing the situation, and won’t bring students back to campus until they’re SURE that they can keep their students as safe as possible (as evident by them cancelling the first month of on-campus classes ~2 weeks before move-in.) Students are also allowed to study remotely if desired (idk about the specifics to request this for First-Years, given that Brown’s making it so it’ll only be First-Years and MAYBE Sophomores in the Summer.)
There are also a TON of students at Brown from California (like 250 students out of a ~1650 class,) so the chances are much more likely that there will be students your son knows going to Brown. It’s definitely a VERY personal decision, but colleges will do their best to keep their students safe.
I agree with many of the points made here particularly the comments made by ucb alumnus. Keep in mind;
Many 3+2 students DO NOT follow through to the targeted end of the program. Financial aid at the STEM school may be limited or unavailable to 3+2 students. The student needs to candidly ask herself/himself how long they would be comfortable being in school because engineering students often participate in either internships or months-long co-ops. The result is that the student’s graduation may be delayed by years. Thus it is possible that a 3+2 student would receive the engineering degree 7 years after enrolling at the liberal arts college. Student needs to decide if they are comfortable with that scenario. It’s best to choose a STEM university that allows for some liberal arts exploration (given the rigor at almost all engineering departments). For this purpose I like U Rochester, Case Western Reserve university), Rennsalaer Polytechnic Institute. I reluctantly suggest U of San Diego because of the many religion classes that engineering majors must endure.
Hmm, 7 years for a bachelors? Then I just don’t see how it’s possible to do engineering if you’re undecided, though I think I prefer the masters route. Have to look into that more…
But one thing stuck out in your post. My kid might actually enjoy taking those religion classes 
and that’s why he doesn’t belong at a stem school, especially when he is undecided.
Actually he’s not interested in a blatantly religious school, but I can see him taking some philosophy classes!
Just so you know even with main stream engineering all schools allow for Breath classes which is pretty much what you want. So those classes in philosophy can be taken. Really pretty much anything that would interest him. I forgot but think its like 15-18 credits (Off of memory). Why don’t you look at any ABET Certified program which will be just about any uni program and just look at the breakdown year by year. You might be surprised at what you find. Your son could also minor is something that is not engineering based that interests him, if that is what he wants to do .
ABET requires that accredited engineering bachelor’s degree programs have a general education component, though colleges have wide latitude in defining what that includes (but it needs to be something; Brown requires four humanities or social studies courses for ABET-accredited engineering majors, even though it has no breadth requirements for other majors).
It is possible that some colleges have specific subjects that must be taken in the general education courses, leaving little or no breadth space for student electives like philosophy or religious studies. If the engineering majors there are voluminous enough to leave no free electives (beyond major and breadth requirements), that could leave no room for such electives.