I have seen audio speakers sold on the fact that a specific audio engineer had tweaked the internal EQ; signed their name to them. If someone later changes the internal [normally inaccessible] settings... the speakers still bear the engineer's signature, and implies that it is they who are responsible for those [now altered] level settings.
I have seen a —screensaver— that forbids modding of it for much the same reason given above; that if any modded version of it were seen publicly, with sub-par art changes, it would reflect badly on them and the quality of their product. because it would be attributed to them alone. No one is going to assume it to be an aftermarket modified product.
Some user modifications of products will change the feature/functionality of it such that it then breaks the developer's prior agreements (with other companies, estates, and individuals); agreements that likely allowed them to make the product in the first place. An example for instance: I know of two particular commercial game editors that export similar playable games; but only one can export a standalone executable; the
other one is a licensed D&D IP product that
requires the editor in order to play the exported game. If it were modded to export a standalone (or browser based) game, it would break their D&D license.
Some games are only salable in certain countries after compliance with their local laws. A user mod that undoes this compliance then bypasses those local laws —potentially causing legal hassle for the developer. So what if they got sued or fined for this, and the game made non-profitable afterwards because of it, or if they lose that country's good-will acceptance for their next title?
A game might have received money in return for including an advertisement; unauthorized mods that remove this ad would then break the developer's agreement, and cheat the advertiser who subsidized them... they won't likely make
that offer again.
Obviously mods that break multiplayer mode by allowing the user to cheat are damaging to the brand and game experience for legitimate users. There are myriad reasons that user modding should not be taken for granted as some sort of "user rights", especially if the user must agree not to, before installing; they take them at their word —and it sounds like a lot of people's word is worthless by their own admission.
This is also what makes those companies that do allow, encourage (, or just turn a blind eye towards) user modding to be so special (and welcome). Those that do usually do so with a EULA, and if it's not respected by the users then they might rightly stop allowing, encouraging, or turning a blind eye in the future.
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TLDR: Don't bite the hand that feeds, and don't shit where you eat.