Lexington and Alma were hardly "towns" in the sense of the word when we think of "towns". These were just a collection of the homes in the area, with perhaps a cross-roads with a few businesses. Not like a "town" in the sense of laid out block after block of streets, parks, school, banks, etc...

At their peak, they had (one source says) "about 200 folks each", but those were not necessarily concurrent (ie.: not a "total of 400 at the same time), as they each had different hey-day time-frames. Even "200" (per town) you have to remember is spread out and includes the colletive population of residents for miles around. I would guess that even today, if you took a slice of the Santa Cruz mountain residential areas (houses that are each far from each other, relatively speaking), you could assemble 200 persons, from a few square miles of what we see now as "residential". I'm sure there was one collective hub with a handful of side-by-side homes to support the hotel, saloons, and other buildings at the namesake cross-roads. If you found that one center where commercial activity, stage stop, etc.. took place, that'd be the place to hit. To just simply wander under the several miles of previous lake bottom, wouldn't put you necessarily on anything historical. Remember that reservoir is 2 miles long!
There was a book written called something like "ghost towns of the Santa Cruz Mountains" (or something to that effect), and they included as "towns" places that were nothing more than a store, a few dozen "residents", and a mail-drop on the store's front porch, etc.... I guess if you get a post office (which anyone could do back in those days by petitioning the post office if you had a collection of a certain amount of neighbors who needed a closer collection spot), and if you had a cross-roads with a namesake, then "presto!" you're a "town"
Back in mission times, locales got the name "village" which were really nothing more than a collection of 7 or 8 neighbors within a mile or so of each other. Same concept with some people's definition of "ghost town". Just because a dot appears on a turn of the century map with a name, doesn't mean "town" in the sense of the way we think of that term today.
Another thing to think about, is that man-made reservoirs are notorious sediment traps. They loose depth over the years d/t sediments that get trapped behind the damn. Of course that would presumably be the deeper portions, closer to the spillways, and perhaps not be an issue further back in the fingers, but something to think of none-the-less. If the "town" is in what has been the bottoms, deeper parts, and closer to the spillways, it's possible that dried up silt will have added who-knows-how-much depth to any targets?