I even looked trying something like this:
system ("$dir_cmd >> out.txt");
but the output comes all mangled up, with so many process's trying to write to the same file

Did you try something like this:

system( "$dir_cmd > out$i.txt" );
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so that each thread would write to a different output file?

Or, since you just want to read output from commands that are running in subshells, have you looked at creating an array of file handles that open "$dir_cmd |"? I haven't tried it, but I expect it would be possible (maybe even really simple) to loop over that array of handles doing non-blocking reads until their all done. (But I'm not running my windows partition just now, so I'd have to try it some other time...)