I'm aware of two potentially problematic consequences to this change:

* making changes to those source files for the modules will not be reflected during execution until after "make" is run
* tricks to inject hooks ASAP (e.g. coverage.py swaps the encodings module) may lose their entry point

For the former, I'm not sure there's a way around it.  We may consider the inconvenience worth it in order to get the performance benefits.

For the latter, the obvious solution is to introduce a startup hook (e.g. on the CLI) like we've talked about doing for years.  (I wasn't able to find previous discussions on that topic after a quick search.)