As to which property has the best benefits in terms of SNAs and breakfast those questions might be better asked in a Marriott thread. With low demand I'd assume it'd be easy to redeem a SNA, but it's just a guess. The hotel restaurants might not be open due to covid so worth checking the hotels current amenities by calling them.

I will say that the St. Francis is a historical hotel and is quite nice, location wise its the best of the three. The Marquis has pretty much always severed the business crowd, as its near a convention center, and location wise is the poorest of the three.

Food options around Union Square aren't great and with covid I'm not sure how many are still open or operating, but there should be something regardless. There are grocery stores in the area.

Bart doesn't operate in Santa Clara so you'll have to take CalTrain and transfer to Bart in Milbrae or take CalTrain to SF and then Uber to the hotel. If I were you I'd take an Uber or Lyft to your hotel, shouldn't cost much more than the four train tickets and is all around a better option.

I'd also echo what gaobest says in that Union Square isn't a great place to be right now since covid has emptied out the city and petty crime has increased in the area. Plus there are a lot of variants and homeless living on the streets in that part of town. Things are slowly returning to normal so who knows how things will unfold. Nob Hill or Fisherman's Warf area might be better locations in terms of things to do and sight seeing.

For seeing Muir Woods you'll either need to rent a car or arrange a tour, it'll be impossible to get an uber or lyft out there.