Since you already had them, Malino, it probably would have been a good idea to teleport them into storage. But if I were you, I wouldn't lament their loss. While it's true that the "lower levels" don't take up much space, it's also true that you can build through quite a few lower levels in the course of one day, with time instants that you can earn in abundance in the spire and elsewhere.
I think each of us have a different playing style, and that's a good thing. We can't all follow the same path. I am in halflings, and have no need yet for sentient goods. I haven't started yet to build for the next chapter's sentient goods because I know I can upgrade quickly when the need arises. A case in point ... I decided I needed an extra dust factory (one of my boosts). I started it and through the use of time instants (what I'd earn in one week in the spire), I had it leveled to WoodElves in a couple days. I'd rather not waste space on a virtually useless building (considering how much more you could get in trade from a boosted factory) for a year or more when it would probably only take a week or less to fully level a manufactory by the time I need it. But as I said, we each play differently. I know a player who loves to have one of each kind of manufactory, for the look of it in their city, and that's certainly okay too. We each build our cities in a way that makes us happy.