It would be very useful to me if you were to add a boolean property 'hidden' to flags and an associated method to programatically hide/unhide flags. It's a cosmetic thing, but I really do find flags quite distracting, most of the time. 

Anything else, ranging from claiming/reserving, to harvesting resources, can be easily accomplished with a

let remoteLocation = new RoomPosition(25, 25, "TargetMapID");
if (creep.room.name != remoteLocation.roomName)
{
    creep.moveTo(remoteLocation);
}
else
{
    // Do stuff like reserving, harvesting, etc.
}

And the desired map ID can be set in an array in the main loop which you then add as a parameter to your creep's role.run() function.

This way, there's no ugly flags on sight and it's easier to clean if you respawn (rather than having to delete flags one by one or adding a for loop to remove them).

You could use a custom flag finder that EITHER returns a visible flag OR returns a position object tied to a deleted flag's memory. Flag.hide could delete the flag but not the memory, and store the position and color into that memory location. Flag.show would create a flag with the old name, pointing at the old memory.

Some tedium to set up, but should be CPU efficient and emulate the exact result you want.