This kind of touches on the problem of whether “organism” or “individual” is even a meaningful unit of measurement at that small scale. Back in my microbio class we avoided those words altogether and used “colony forming unit” (CFU) for any sort of quantitative analyses. One colony generally counts as evidence of presence for one CFU.
In my opinion, it is better to go by practical usefulness rather than following policy to the letter. iNat’s guidelines were never intended for this kind of observation, so I think they should have little jurisdiction here. For practical purposes, an observation should be allowed to reach RG if it satisfies the standards of sampling and identification of whichever particular field it would fall into. And cultivating and isolating colonies is essential for morphological or biochemical identification.
It would be ironic that following more or less standard research procedure would prevent an observation from reaching research grade.
(That being said, I think whether these observations reach RG or not is pretty irrelevant from a data-quality POV for various reasons. Most cannot be IDed to species or even genus, so they probably never become RG anyway, and I don’t think iNat is used much by researchers for data on these organisms)