In the MLAG configuration documentation there is information that if I want my switches to be a root bridge in STP I should set the same priority on both MikroTiks, as an example is the value 0x1000. But if I don’t want them to be a root bridge, should the values also be the same but can they be higher? Or does it then no longer matter and they don’t have to be identical?
They have to be identical because, to the rest of the network, they are one switch. Yes, you can make the priority higher (thus lower on the totem pole as far as the rest of the STP network sees them).