From my experience does cperl not attempt to format nested data structures

It shouldn't, but it does. As you suspect, CPerl mode mistakes the nested data structure as a control structure, which it reformats intentionally (see example here). It just takes a wrong turn in the function cperl-fix-line-spacing. Therefore, it is rather obvious that the issue doesn't occur with arrays: square brackets can't be confused with control structures.

If you want M-x cperl-indent-region and M-x cperl-indent-exp to do indentation and nothing else, set cperl-indent-region-fix-constructs to nil.

In reply to Re^3: How would you indent this? (cperl-indent-region) by haj
in thread How would you indent this? by no longer just digit

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