https://na.finalfantasyxiv.com/lodes.../housing_land/
Ok, according to the rules stated in the above link, while you can only "own" one FC plot per world per service account, the actual limitation seems to be on you purchasing a plot. You can technically have two characters on two different FCs with two different houses.
The question is whether you can then be given ownership (either automatically or manually) to both FCs. Does anyone know if there is a service account limitation on owning an FC? If you can own both FCs, then there is no actual limitation stated in the link above on owning both houses as well since you did not need to purchase either plot.