I'm considering trying to make a mod that lets you mess around with time. As well as slowing it down/speeding it up, I'm hoping to be able to make the player be able to age companions up or down. While I know there's a console command to rescale the player, is it possible to do something similar to NPCs without needing to quit the game, enter the geck, save the mod again and go back in? And is it possible to change the body model of an NPC mid-game? I could just do it as clothing, but I'd prefer to not need to worry about clipping and using up clothing slots.

AFAIK, any console command can also be executed as a script within geck. If you have written scripts, for example as part of a quest or a complex object, then you can try setting a quest stage to change the size of a character. Another approach may be to have several NPCs, with different appearance, and use enable/disable to switch between them. I have done this with one of the characters in "Decisions With Regrets" (link below), where a character has an accident at one point and thereafter has a different appearance.