PHP causes so many issues because of the fact that it uses the same syntax for both arrays and dictionaries/maps. [] (or array() in older PHP versions) always JSON encodes to [] because there's no way to tell if it's supposed to represent an empty array or an empty dictionary.
Eh. It works just fine. I agree JSON encoding is weird but if you use it the recommended way (just use a StdClass object and throw on the fields you need) it works fine. Someone added half assed support for weird PHP arrays that usually works and is generally good enough.
If you read the docs for json_decode, the default behavior is to operate with stdClass - I too prefer working with associative arrays because of their power but... that kind of just reinforces how useful they are. PHP can give you the full Java class system if you want.. it's just a pain and useless in most circumstances so we all just toss around associative arrays.
Perl had $[ (yes, just those two characters) to allow setting of the first array index, but it's a fatal error to put anything but 0 into it now.
Of course, since Perl arrays can be negative subscripted from the last element, you can stand on your head and index the array negatively from the wrong end. -1, -2, -3 etc. Use unshift to put things on the beginning (logical "end") of what you're doing rather than the usual push. Presto, a 1-based array (up to sign, anyway).
You may wish to file this under "stupid, but it works".
People with more time / more need for something that looks professional, would probably be better off writing something that uses tie instead. (Or, yes, yes, a different language entirely, hush now.)