iTerm: How to make options (e.g. -r) after filenames work?

It's not up to iTerm, it's up to each individual command program (like rm, ls, etc) how to parse its arguments. The traditional convention in unix commands is to require options to come first (before positional parameters), but the GNU project has adopted a convention where they can come in any order (except that -- indicates the end of options). macOS avoids GNU software as much as possible (for licensing reasons), and uses mostly bsd versions of commands... which (mostly) follow the traditional options-first convention.

You can install GNU versions of commands if you want (e.g. with homebrew). But there's a problem: because the GNU versions are different, you risk breaking scripts that assume the macOS-standard commands. To avoid this conflict, GNU versions are usually prefixed with "g" (e.g. gawk instead of awk), so you'd have to get used to that instead.

So, my advice is to get used to putting options first. It's the way most of the commands on macOS work, and if you try to change it you're just going to create other problems.