Yes, generally rigor increases odds for the lowest-probability product, but there's an interface for mods to specify a product manually. And in fact this mod has to specify holmium ore, because there are a few scrap recycling products that all have a 1% chance. For vanilla the only recipes are uranium processing (U-235), yumako/jellynut processing (seeds) and scrap recycling (holmium ore).
A productivity penalty is an interesting idea, though (like quality) there'd be no effects from net negative productivity. It is a more serious tradeoff than just energy consumption. My main concern is that a prod penalty could devalue the first level or two of an infinite productivity research; for example if all my scrap recyclers had -10% productivity from rigor modules, the first level of scrap recycling prod would do nothing. I have a strong preference to avoid that kind of thing since it feels like a punishment. But it's too intriguing an idea to not take seriously, and maybe the buildings with +50% productivity built-in offer the perfect solution.
In the end I think most of the potential in rigor modules will be with modded recipes. I do really like using rigor to kick-start nuclear power or Gleba soil production, but the only vanilla recipe where rigor modules can help with science is scrap recycling. And even there, if you're using legendary prod mod 3s then holmium is no longer your bottleneck wayway!
Crucible's recipes are designed for rigor, and I'd definitely love to see other planet mods (or content mods generally) run with the idea. But I'll bet there's also lots of potential for some tweaks to vanilla recipes to utilize rigor modules.