Covered farms and as well as the other 7 buildings you can buy from the Opal Illari can be found as rewards from Secret Missions. Please note Secret Missions don't show up on the Over-Map and have to be checked manually to see if they are available once you find one.
Also, in case you missed reading it, x4000 (Chris) noted in the release notes for 1.109 that when starvation goes live (it isn't at the moment) covered farms will be added retro-actively so your existing NPC's won't starve to death before you can find enough of them.
Places you can find Secret Missions:
- Surface chunks that are colored yellow instead of green on the region map. If a region has one it's usually located 4-5 or more surface chunks into a surface region and there is, in my experience at least, only one of these per surface region.
- Secret Mission rooms inside buildings, usually larger ones like lava towers for example. Again the room will be colored yellow on your building mini-map and there is usually only one, if there is one, per building. Mystery puzzle rooms share the same color on the mini-map, just mouse-over the room on the mini-map to find out which it is. Mystery puzzle rooms and Secret missions are not mutually exclusive so you may come across buildings that have both, though it isn't that common.
- Underground caverns rooms that are colored yellow on your cavern chunk map will also contain Secret Missions. Again as with the other two, if a Cave level has one there will usually only be one in level itself but lower cave levels should have a chance of having one of their own.
Some Secret missions will be rescue missions but if they are they will have the additional label as such and I have seen a Secret Mission and a Secret Rescue Mission in the same cave level. They were side by side and even shared a direct cross-connection to each other. I assume this can happen in buildings as well but I don't remember if I've seen it yet or not.
As far as finding secret missions inside underground buildings goes, I'm not sure it happens that often as most UG buildings tend to be small so the chance is fairly unlikely.
