There's no reason to discourage parses and modding since these don't affect other players.
In 'this' game it's not such a big issue, but the ability to change the texture and models of anything at will can be absolutely damaging to some mechanics--especially in PvP situations. Imagine playing a PvP game where you can repaint the walls invisible, or change the model of a flag to that of a 50 foot neon-green arrow.

Or why buy mog-station items if you can just mod your shirt to look like something others had to pay 18 dollars for. The point is, modding isn't entirely innocent. Though nude mods are probably the least impactful they can get.

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The impact of parsers can be (and has been) explained in other topics, so I won't even touch it. Suffice to say, Square-Enix's ToS shouldn't really be treated as "these third party programs are ok, but these other ones aren't." If they do decide to crack down on them--they'll probably take all of them in one fel-swoop.