At O(million), the problem wrangling it has more to do with how well its architected and written than it being Python. Python is at least easy to read. Its major deficiency is the lack of annotation of parameters, and that's something that could now be fixed... but it isn't going to be fixed in that much historical code.

It you are trying to get performance out of it (which doesn't really hinge on whether it's a million lines of code), then Python might be the wrong choice. But you can always write it in Rust or C and give Python an API to the functionality.

I agree that packaging is a mess. Fixing that mess with modularization in Java took a long time, and most other languages have that problem, too.