"The kitchens in their houses are small."
Translation:Kuchyně jsou v jejich domech malé.
You can find use for almost any word order in Czech sentences with the right meaning and with the right stress. Your word order is not correct for a simple announcement that they have small kitchens.
But if you put strong stress on word "malé" and say that when currently reviewing photos or plans of their houses, I would find that usable.
With stress on word "jejich", your word order implies you already know kitchens in some houses are small and the new thing you are announcing is that it is in THEIR houses, where the kitchens are small.
With neutral stress I'd say your word order implies that it is in their HOUSES and not in some other their thing where the kitchens are small (= weird).