I see what you're saying, but there are differences between retainers and custom miniatures.

First, the retainers use models and gear that are already present in the game, which should be limiting their footprint. Granted, you're customizing their appearance, but all options already exist. Keep in mind too, that you're only given three, and have to pay extra per month for any extra you want--I assume because of the resources they take up.

For miniatures, they would have to replicate all gear and character models at that scale, which would take space, and then be able to save however many per player they allowed, which is more. It would hog resources pretty quick.

Granted, I'm not a game designer, but it's kind of the same as in relational databases.