I'm not going to say this happens on every single island, but I think it has happened on pretty much all of mine. I generate random islands for my sandbox games. Good land for growing tobacco will usually show up on any sloped ground, and maybe on a very few flat spots on the island. But every map I recall had the palace sitting right on top of good tobacco land.

Does El Presidente have some sort of hydroponic operation going on in the basement?

No, the basement is full of money, remember? That's where el Presidente goes to swim around in his hoards of cash.

About the tobacco, I haven't seen that happen much. A lot of it depends on how you set up your island with elevation and such. Do you use a lot of higher eleveation or mostly flat? Do you have a lot of vegetation and humidity or not? There's a lot of room for variation in this game. Maybe you should try using larger, flatter islands. That'll give you more than enough space to develop any industry you want.