Welcome to the community. I contacted the developer last year and they assured me the Harmonaig quirks are by design to match the quirks of their hardware module so that students will face some of the same challenges as in the hardware world… At least that is what I understood.
I emailed jason at some time too, I copied his answer to the forum. It was about: “I have to add 0.0001 V to the unquantized CV to get the harmonizer to work as I expect”.