As mentioned above, an alternative idea - which would get around the issue of rebuilding harvesters of variable marks - would be to replace the Harvester upgrades with a Harvester Efficiency Enhancer, which would sit on a world and increase the production of all harvesters on that world. Static structure, pretty durable, small cap, and either needs a 1/planet cap or needs to be coded such that only one per planet actually has any effect. Mark II and possibly III upgrades do the same thing but better, but have even lower caps; and you can't stack a Mk I and an Mk II on the same planet (or rather you can, but only get the benefit of the Mk II).
That's your optimal small-empire choice (it doesn't prevent you having Logistics stations, and you can have one on your homeworld). The Economic Command Station is uncapped, and is a better choice for large empires.