The Muni Metro lines that run underground on Market St. ARE run by MUNI so you can use your passports there. You might have to show an agent your passports but it's included. The old fashioned streetcars, E & F that run on tracks are MUNI operated too.
The passports are good for all city transportation
I don't think so. Metro trains are operated by BART, but cable car and city buses are operated by MUNI.
Yes
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