The Nanobots issue affects Nanobots 2.0 specifically and also occurs in vanilla saves. Although my Compatibility page doesn't say it, the Patchset is also compatible with Nanobots 3.0. Whether you trust a mod that claims to be "AI-improved" is up to you, but I can confirm that it does insert modules properly.
I can't reproduce the issue with Helmod (although I did find a completely unrelated error in my testing), so you'll have to walk me through it, but I suspect this error is also not exclusive to the IR3 Patchset. I never formally tested Helmod for compatibility, but I know that Factory Planner works.