You were right to be skeptical — 5.8.6 didn't fix it because the crash happens during the data stage, before my data-final-fixes step ever runs (your log timing at 0.313 made that clear).
The real cause is stdlib2's Data/Recipe wrappers attaching function-carrying metatables to the prototypes; pypostprocessing serialises data.raw and chokes on those functions. The fix other stdlib-based mods used (Reverse Factory, etc.) was to drop stdlib from the data stage entirely, so that's what I did in v5.8.7 — the sounds, equipment chips, roboport-interface, and bob-mod recipe edits are now built with native data:extend. No stdlib left in the data stage.
I can't run a full Py set myself, so I'd really appreciate a load test on 5.8.7. If it still crashes, a startup log would help a lot — you can grab it from %appdata%\Factorio\factorio-current.log (Windows) or ~/.factorio/factorio-current.log (Linux/Mac), right after the crash. Thanks for sticking with this!