Ummmm… Since they are separated from the houses like your wish, no longer providing population, the Incas would have to pay additional resources to gain the food trickle they should own originally. The current Inca economy structure bases on the food trickle existing there, so becoming to lack the trickle and to cost more resources would make the Inca offensive delay.
On the other hand, they should not be similar to the Porcelain Tower. The Porcelain Tower is limit to up to only 1, unable to be rebuilt, its mix of resources contains less per type of resource, and its efficiency would keep low if it is built in the early game. If you wanna make them able be upgraded, they should have a lower initial food trickle and get better and better as Age gets advanced, instead of just making them generate other resources in as bad efficiency as the initial one. Anyway if generating other resources is expected, there can be a new card named Bursera Graveolens, which make Kancha House also start to generate wood by 0.35 per second and slowly heal nearby friendly units. This card is also listed at here.
I like the idea about llama, but I prefer to make your “normal houses” really normal than having other special ability again. The Kancha House can be set to able to choose the option between resource trickle and automatically generating llamas.