Uber and Lyft quote a flat rate - not necessarily the zoned flat rates referred to above. If a trip takes significantly longer (in miles or minutes) than they assumed when quoting the rate, the fare can change. This is principally to protect both rider and driver if the rider asks to make a stop, or go out of the way. (Lyft allows a multi-stop trip, Uber does not, so if two people get in a car and don't go directly to the final destination, the rate won't quote accurately. I'm not talking about "pool," I'm talking about two people leaving the same location and going to different locations.)
I would indeed think that if an Uber took the tunnel, it might revert to a higher fare, but it should be fairly simple to dispute this with Uber.
I take Uber from the airport several times a year, going to Orleans, which is on Tropicana about a mile west of the freeway. I almost always use the pool option, so they might take an out-of-the-way route and I wouldn't notice, but usually they come right out to Paradise and left on Tropicana. I think that with pool the rate is guaranteed, because you can't alter the route once the trip starts.