So? Use a virtualenv and stop worrying. These 26 dependencies will be separately updated and maintained, who knows what warts are sitting in the monolithic perl scripts.
There are pros and cons to both sides.
Would this make you feel more like you knew what was installed on your system? Would you have felt the need to look at the source code, including the source code for any embedded dependencies, in, say, a 'vendor' or 'lib/dist' directory or something?
What are the plusses and minuses of each approach? There are some plusses and some minuses either way. After considering them, do you still have a problem with the 'new way' of doing things, where a program might install along with explicit dependencies via pip (or rubygems in ruby) separated out in a different place in the file system, vs. embedded/bundled dependencies?
`pip install awscli` just installed 26 other modules besides awscli. Now I feel a little obliged to go check out those 26, as well, to see what they are.
I agree about not re-inventing the wheel. But the amount of stuff installed is definitely a considering factor when choosing between two seemingly identical scripts.