Indeed. I managed to program Python a few years before really taking note of that difference. Couldn't understand why my data structures kept being corrupted. Ahem.
FWIW, in Perl 6, references do not exist at the language level. At the implementation level, you could argue that everything is passed by reference. Perhaps you may find https://opensource.com/article/18/8/containers-perl-6 enlightning.
It's been a long while since I've developed anything serious in Perl, but the main difference I find between Python and Perl, aside from the syntax, is the value/reference split: Python makes every (passed) value a reference implicitly, Perl uses references explicitly, that can affect an architecture in important ways.