It's not really a sandbox. It's a hub system which lets you choose the order in which you do events. Other than that, it's just a regular VN where most of the choices are for dialogue flavor. There are no free roams, no resource management, and there's not even very much branching.
Honestly, the "Sandbox" tag is even less of an accurate descriptor of Desert Stalker than the "Female Protagonist" tag. At least with the FP tag, it's justified because there is a small part of the game from Shani's perspective even though 90% of the game is Zaton's perspective. "Sandbox" just doesn't fit at all.
I am not sure I agree with your conclusion. When I just read people saying this was a sandbox I was surprised and thought what you wrote but after thinking a bit more, I don't know. There's truly a sandbox feeling attached to the game that I can't entirely...
At the end of the day, you choose what to do, mostly the order in which you do it, you can make every quest in a different way, with different conclusions and different consequences (for example, you can lose quests as a consequence of some choices).
Sure, there is a main story line but for now, in this update... I'd say sandbox fits. Not greatly, not exactly, not perfectly. But I am surprised to admit that it fits to some degree. This game has a lot of sandbox elements mixed.
Maybe it gets more defined as they complete the game.