...are different?
Particularly PERL where the ~ character opens and closes a string quote, but is also involved in other functions, which don't want the same highlight applied.

If there was some way to all for (say) qq~ as the opening quote marker, and ~; as the closing one, so that =~ isn't picked up in error - you get the idea?

Perl has an alternate quote syntax where pretty much anything can be a quote character. It's useful for avoiding "backslashitis" in situations where a string contains embedded quote characters, but it's hell on syntax highlighting.

s_m_b, please chant the following mantra:

Nothing but perl can parse Perl.

Perl's syntax is much too flexible and context-sensitive for a general purpose editor to get the highlighting perfect. Even Perl-specific IDEs have their share of problems. UE can get most things right (with a little tweaking), but not everything. It's better to accept this than to fight it.

Sometimes you can adjust your coding a little bit. e.g. use qq to turn single-quotes into double qoutes:
Which works unless you embed both single and double quotes.

Didn't I read somewhere that Perl is the only language that looks the same before and after RSA encryption?

SCNR,
Tim (Python aficionado)