The replacement character itself does not matter, but the problem is safe_extra does not normalise - (and .). Under safe_extra rules, a£b and a-b are not equivalent—a£b normalises to a_b, and a-b is a normalised form.
This is a problem for a package currently using - in the extra name. For example, if a package declares an extra a-b and dependency foo ; extra == 'a-b', pip install package[a_b] currently does not install foo, while a PEP-503-based rule will. This is more problematic if the package has both a-b and a_b declared as extras, although this is so fundamentally user-hostile I’d hope no package would do it. The same applies to .; foo ; extra == 'a.b' can currently be selected with [a.b], but PEP 503 would allow [a-b].
BTW, there an additional minor difference between safe_extra and PEP 503 normalisation. PEP 503 specifies any running non-alphanumeric sequences be normalised into a single dash, which means a--b becomes a-b, but safe_extra only replaces running non-safe sequences, so a__b normalises to a__b. But again, anyone relying on this is probably too user-hostile to be a meaningful consideration.