I think the reason is because it is more effective to update their ingame appearance and skillset together with their lore.
If they give them a lore update now they would need to work with the current visuals,abilities and personalities of the champs and considering how much VGUs can change nowadays I'd say that could be rather limiting for the lore.
Likewise their updated lore would also be limiting for future VGUs.
If Morganas lore makes a huge plot point about her being unable to fly,then her future VGU cannot include functioning wings.
If the lore makes a big point about Morganas black shield not being able to block physical attacks and then her VGU changes it into actually blocking physical blows as well,then that would seem really odd in the lore.