I don't use blueprints a lot and even less habitat blueprints, but my understanding is that when you place a blueprinted item, at least my experience with grid items, it lines up the lowest item to the ground level. I always find this when copying some item I have made that has parts extending into the ground, that I have to re-lower it into the ground before placing.
If you are just looking for a simple habitat to copy-paste for farming with no aesthetic preferences, probably if you can create one that has no elements below your normal ground level, which I don't know but might even include terrain being lowered, water that sits in the ground, or habitat barriers that extend into the ground, then inserting it will result in it being at ground level.
When it comes to copying things that you want to have things extending into the ground but want to neatly lower it to the right level when re-using, adding a marker item e.g. a flat piece off to the side, which should be lowered level with the ground, can help you more quickly get things lined up.