Do OS X upgrades install packages that shadow pack

Question

After upgrading to Mavericks (OS 10.9), I found that the locations that Apple's Python (2.7.5) was using for many packages I had installed earlier had changed,¹ and that several had been "downgraded" to older versions. Confusingly, I found that updating these older versions (using pip which I use to maintain my packages) was prevented by the presence of unused but current versions these packages,² and that deleting the new (but older) versions that Mavericks had installed was necessary.

What's going on here? Did Mavericks just come with some commonly used packages (like mathplotlib) that it put in the .../Extras/... folder where they shadow versions I had been maintaining in .../site-packages/? Using pip seems to have fixed this problem, effectively clearing out .../Extras/... of (often slightly old) duplicates of my packages in .../site-packages/, but I want to confirm that I'm doing the right thing, especially since this seems to happen every time Apple updates Python.

^{1: To /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python
2: Still present and undisturbed in /Library/Python/2.7/site-packages/}