had the same issue
minimap was taking forever to genarate (well over 12hrs) 16km*16km world partition map and had to cancel it as it was taking too long even after removing all skyboxes , same
then i found this :-
in UE5.3 add volumes (near end of list) is worldpartitionminimapvolume
add it and set the size and position of it to fit your landscape aria
run the build minimap and presto map done in under 10 mins with all the skyboxes still present in the level