I've changed review to "Almost sandbox", hope you like it.Harem Hotel and Minecraft could no be further genres from each other. Comparing them is so strange. Harem Hotel is closer to Persona 5, which is also a visual novel with sandbox elements.
Honestly, almost every game I've played has a linear story. They are designed with end goal in mind. HH just happens to have more dialogs. I've never played Persona games, sorry. But you can take a look at any other game to see the picture: FarCry games have linear story but free world to explore, Starcraft has linear story but sandbox gameplay, GTA has main storyline, Need For Speed has linear story but you can finish it with any car...
Ofcourse there are some exceptions, where you have to choose one possible ending, like in Fallout or DeusEx. But those games are so few that I consider them minority.