Perl is not an acronym. The name came first, the words that supposedly make this acronym came later. It's not written "Perl" because it's pronouncable - the name was picked to be
a pronouncable word, and one with positive associations ('Gloria' has been a contender for the name of the language, and 'Perl' was almost called 'Pearl' - but it turned out that was already a language with that name (in fact, there are already several languages with the name 'Pearl')).
PHP on the other hand is an acronym. IIRC, it used to mean "Personal Home Pages", although I think it now stands for something else.
The fact that Perl is often written as PERL becomes from the 'joke' in the first manual page of Perl (which as survived till today) where the NAME section says:
perl - Practical Extraction and Report Language