Unlike Los Santos, which is more or less a condensed version of Los Angeles missing a few parts, Sandy Shores, Grapeseed, and Paleto are mongrels. As such, the ways in which you might identify an area of the map sometimes don't align as they do in Los Santos. For example, the road layout, buildings, and geographical features of Los Santos are, generally, purely those from Los Angeles, Ca. If you are in your car parked in front of the 801 Tower, and you desire to head to the Santa Monica pier; you don't have to look at the HUD or in-game map to get there even if you are new to the game, if you are familiar with Los Angeles. You'll know which direction to go and can get yourself in the general area simply navigating by landmarks, as one does in real life. That is not true in the other areas of the map.
Sandy Shores is perhaps the most clear cut of the population centres located in Blaine Cty. Sandy Shores shares its general layout, and many of its locations with the real life town of Bombay Beach, Ca. The shape of the Salton Sea(Alamo Sea) when turned and the relative location along the shoreline also suggests this. However, many of the more prominent locations are from other areas as well. As discussed in the GTA 5 Cars thread, the abandoned motel, marina, and the artificial harbour are all locations from nearby Mecca, Ca; about 15mi Northwest of Bombay Beach. Others are representations of locations in Niland, Ca, and Desert Shores, while the main boulevard is much like one found in Thermal, Ca.
Generally, the area in and around the desert represents areas of the Imperial Valley, with most structures being copies of those found in and around real life Mecca, Niland, and the unincorporated villages surrounding the Salton Sea. Senora Nat'l Park in game is considered to be Joshua Tree Nat'l Park in real life, north of the Salton Sea straddling the Mojave and Colorado Deserts, just north of the Sonoran Desert. Clever haha.
The fields in Grapeseed are a rather common open field layout that make up much of the Imperial Valley south of the Salton Sea. The buildings and structures along the 'downtown' area are mostly from Lamont, Ca, which is 250mi NW of the Salton Sea, north of LA in Kern Cty near Bakersfield. Some are from Somis, Ca, which is also north of LA in Ventura, Cty, also nowhere near the Salton Sea. At least one location matches Fillmore, Ca, also in Ventura Cty.
Paleto Bay gets even more odd. The tram is Palm Springs Aerial Tramway, which is located northwest of the Salton Sea, and runs up San Jacinto, but not to the peak as in game. Some of the geography is very similar to Idyllwild, while the main drag is mostly buildings from Lamont, Somis, and Fillmore again. The police station is from Fillmore, while the church(same church all over the map just turned different ways) and liquor store are from Piru, Ca, also in Ventura Cty. None of these locations are anywhere near the sea. Some of the area geography is very similar to Big Sur, with Paleto Point being similar to both Point Sur and Point Conception, both hundres of miles from Palm Springs and Ventura Cty.
Does this make it any clearer?
Going back to my opening paragraph, what you identify these places as depends on how you define what criteria used to create such identity. Geography, buildings and structures, road layout, relative location to known landmarks? What takes more precedent in the decision? It is tough to answer. There is not simple answer for many of them, without leaving out many references in many locations. I, personally, have something near 500 in game locations identified and researched. This is what created the bases for the tours that I have hosted, and understanding the relationship between these places and the game map is one of the things that makes the game enjoyable for me.
You could call Sandy Shores Bombay Beach, Mecca, Desert Shores, and perhaps a few others; and you wouldn't be wrong. You could call Grapeseed Idyllwild, almost any town in the Imperial Valley, or even parts of Ventura Cty and not really be wrong. You could call Paleto Big Sur, Palm Springs, or possibly even parts of Santa Barbara Cty and not be entirely wrong. It could depend upon which street you are standing on, or building you are in front of, or bridge you are crossing.
Anyway, I go into a lot more detail on the specific places in some of the tours. If these types of things are of interest, stop by one of them.