Never, in all my two dozen playthroughs of StarSector version .95.1, have I found a planet suitable for regular Soil Nanites in a system I'd want to settle. I can find plenty of planets that technically can take Soil Nanites, but why would I settle a single Poor Farmland desert planet by itself? I can probably find a Terran World with Rich Farmland, although it's probably "polluted" with Organics or Rare Metals, and will have other planets in the system. So, you know, objectively superior in every way except I can't use Soil Nanites there, but it would produce more food anyway.
I can't speak for .96 yet, because in my two playthroughs I haven't explored literally every planet in the sector, but I don't remember the last campaign that I ever had a reason to use Soil Nanites. The exact combination of "already worthwhile to farm" combined with "not worthwhile to mine" needed means that I'm statistically never going to use them.
A "Perfect System" would have a mining planet, a low-hazard barren planet to use as a forge world (the first two are often the same planet), a gas giant for fuel production, and a Terran or Terran-Eccentric world to supply food. I don't remember the last time I've seen a "Perfect" system, I always settle for, ehh, good enough. If I waited until I explored the whole sector before I started colonizing, I probably still wouldn't find a perfect system, and once I've explored everything, the campaign is basically over.
My Soil Nanites, unlike any other piece of Domain Tech, just sit in my planetary treasure vaults next to my 200 Arbalest Autocannons and my 15000 units of scrap metal until the heat death of the universe or at least until I get bored and start a new campaign. The description for Soil Nanites states, unfortunately the inbuilt safeguards on this unit seem to be operational. We can get Corrupted Nanoforges, and hope to replace them with the rarer but vastly superior Flawless Nanoforge. So we should be able to get Hacked Soil Nanites that can be used on any planet with the right climate. Make them five times as rare, fine, make them generate an obscene amount of Pather interest, okay, they probably would consider it a hideous corruption of sacred nature. At least I would ever use them.
Or maybe make an optional quest where Gargoyle or somebody like that offers to hack your Soil Nanites if you do some huge favor for them. Come on, Gargoyle would totally hack some nanites just because you bet him he couldn't do it, much less if you offered him a pet rock Alpha Core or swung an antimatter banhammer on some online rival of his.