This could get mildly annoying every once in a while when there are legitimate non-clashing names. A better metric/typo recognition technique is probably possible. Or else some manual process for requesting exceptions (maybe with a tiny fee to help fund the overall project) would also address this problem.
EDIT: Just downloaded and read the thesis abstract. The author actually suggests the first idea: "The analytical part generates ideas
for countermeasures that allow repository maintainers or users to detect typosquatting attacks
in the future. For this purpose potential typosquatting candidates could be generated for each
legitimate package name with the help of the Levenshtein distance algorithms or Bayesian
networks. Another option that can be considered is the Metaphone algorithm."
Who would use that?
Package managers have humans to deal with edge cases (removing malicious packages, investigating package errors, etc.) and this is no different. It wouldn't significantly increase their burden because only a small fraction of package names should require human validation.