I see the logic of what you are saying, but for this to work, it will be important to make sure that consumers of such files understand that they must pay careful attention to the use of dash versus underscore in the same position in various file names. See e.g. this image from PyPi for your example:
It would be an interesting empirical exercise to have a number of people go to the page with these two files (supposedly to learn about ways to download them) and then test to see how many of them notice the difference in the separators for these two files. Until I read your post, I would always have expected that the separator for files from the same author to be the same across files. So I would almost surely have failed such a test.
If many people fail, it means that we face a challenging problem with typo-squatting. Perhaps it would be useful to scan PyPi for cases of file names that differ only by a substitution of a dash for an underscore or vice versa. Such a scan would not generate a false positive by identifying the two files on this page. If it turns up any instances, it might be a good idea for someone to take a close look at them.