Not offering an opinion, merely sharing my experience, and stating that cuts can potentially count probably wouldn't cost anyone 1000's :)
Our neighbors had similar issues where their clones in rapid rooters counted, and the officers made them trash 40 or so clones that put them over to get them back in check. Technically we were 1 plant over with the clones and he did mention that he understands that clones have a mortality rate and they weren't going to bust chops over such a small infraction, though it was noted on the inspection paper.
I think the reason they're counting the "stick in a cube" as a plant is that they realize what your intent with that is and though it might not have roots now, that stick will more than likely turn
into a plant one day and need counting. They made mention about our trash as well as we had some leafs and stems that weren't shredded and that "people can go through your dumpster and make clones from your discard". So apparently clones are quite the concern for at least this agent.
Not sure what you mean by regular officer. We've had both inspections, our state inspections which was a single officer who was in our facility for maybe 20 minutes tops. And our city level inspection which
took roughly 2 hours, and was much more in depth including a team of 4 officers, though our city inspection was before the
supposed cutbacks so could be reason for the larger numbers?