If they require some sort of a seal or tag or lockout, they'd have the necessary seals/tags/locks on hand and the people to put them on.
I suppose if you are unsure, you can always call the ferry company and ask your questions of them directly. That will give you better (at least more specific) information than any general forum post could.
In terms of tunnels: while the regulations do vary considerably from tunnel system to tunnel system, very generally speaking propane is commonly regulated or forbidden when the tunnel entrance is at the high points of the tunnel (i.e. it's a tunnel underneath a city or a body of water) and less commonly so when the entrances are at the same or a lower level (i.e. a tunnel through a mountain). This is because propane is heavier than air, and in the first case it tends to settle down in the tunnel if there's a leak, while it more readily dissipates in the second case.
The Boston area tunnels are another set that prohibit propane (even if turned off). The signs don't specifically mention propane or RVs; they only state that no hazardous materials carriers are permitted, which they are quite clear on.