Well I can't speak to some of the others... but Conda doesn't work at all on ARM today (maybe that will change with the new ARM Macs, though), which is annoying if you want to use it on, say, a Raspberry Pi for hobby projects.

Additionally, many scientific Python packages use either pre-compiled binaries or compile them at install-time, for performance. They're just Python bindings for some C or Fortran code. Depending on what you're doing, that may make it tricky to find a bug that only triggers in production.