If you make a Githyanki, and choose to replace the origin proficiencies (martial prodigy), then the resulting options don't let you select light or medium armour. Is this a bug or a feature?

This is RAW from Tasha's. There is no option to replace a proficiency with any armor proficiency.

But you don't have to replace the armor proficiencies, so one could choose, RAW, to keep the armor proficiencies and swap round any of the weapons for weapons or tools. It's hardly a major thing, I'm just going to quickly create a homebrew race for my use case. But interpreting from Tashas, I think it should be possible. 

Hmm, actually, poking around some more, I see what you mean, but I can get it to work for me. First, check that you're not already getting armor proficiency from another source, like your class. If there's literally nowhere else that you could get armor proficiency from, toggle the origin proficiencies off and then on again, and check the bottom two entries in the list again. The dropdown is doing that thing where instead of telling you 'you already got light armor proficiency from being a cleric' it just doesn't make it an option in the dropdown. But when I switched to sorcerer and reloaded the dropdown menu, the armor options appeared.