I wouldn't say a mod that helps the player is necessarily unfair. The use of unmodified Nintendo-brand GameCube controllers is a de facto standard, and not necessarily the "best" one (there is no objectively best or correct standard; it depends on what the players and community want). If the vanilla GameCube controller had perfect wavedash notches in it for some reason then that would be the standard. What would your opinion on the notches be without the accessibility factor (in a situation where arbitrarily notch-modded controllers were very easily available, for prices reasonably similar to that of normal GameCube controllers)?
In the case of spring removal: the in-game benefit it has is to disable lightshielding (preventing it from happening unintentionally), and it also has the physical benefit of reducing the time and force it takes to reach a digital press (allowing you to react with a hardshield/powershield slightly quicker/better). Disabling lightshielding is something that can be done by simply holding the trigger down as the controller is plugged in; that's never going to be banned (mostly due to it being unenforceable). The physical benefit can be achieved by holding the trigger down as the controller plugged in, and then keeping it nearly completely pressed down (just above the level of a digital press; at the same height as the trigger would be without a spring); the reason no-one does that is because it's physically uncomfortable and because removing the spring accomplishes the same thing without that problem, but it's certainly viable. That mod can be functionally replicated through an easy, temporary, and impossible-to-ban method; modifying the controller for it just makes it easier and more physically comfortable to maintain (if you want the full benefit and not just the removal of the possibility of accidentally lightshielding).
I remove the spring from my trigger, and the most valuable advantage by far for me is the reduction in physical strain, especially with triggers that are stiff or with playing Luigi (or other characters that wavedash a lot). I would be very unhappy with having to hurt my hands more because of a blanket ban on controller modification.
Any kind of ruling on mods is going to be arbitrary to some degree, even one that bans them entirely. There are complications caused by the fact that a lot of mods functionally overlap with normal controller wear. Button and spring resistance can be heavily reduced though normal use (what's your opinion on cutting trigger springs down, rather than removing them entirely? I ask because a stiff spring of artificially reduced length can have the same resistance as a worn/loose spring of its original length). Technically you could make almost any kind of modification to your controller's stick gate just with the control stick friction without even disassembling it, though realistically the creation of any useful notches isn't going to happen; wearing the existing notches away is definitely possible though (look at Silent Wolf's controller for an extreme example). I can't see the logic in banning a modification when it's done intentionally but not when it happens through normal use, since in that case the problem clearly isn't with the unfair advantage the modification provides.
A mod that improves a player's gameplay is unfair in the context of them having enhanced physical ability compared to someone using a standard controller. Could it be said that removing springs is "more fair" than custom notches because it is more accessible? I guess, but if we're using the non-modded controller as a standard then any type of mod is unfair, and non-modded controllers are BY FAR the most common used by competitors. The number of players who have removed springs greatly exceeds those with custom notches, but even they are only a small percentage of the community. If you go up to every Smasher at your average local, the vast majority will have a totally unmodified controller. Telling those players they have to mod their controller or play with a disadvantage should absolutely be considered unfair.
If we lived in a world where more than 1% of the community used different controllers, I can absolutely admit that the debate would be different. If there were respectable third party controller options available from the game's launch that players grew up using, it would obviously impact how fair or unfair using them would be. I would still hold the position that the standard GameCube controller should be the standard since it's what the game was designed for, but it also just wouldn't matter as much. We have seen this occur in the traditional FGC where games that were
designed around arcade sticks have failed to control what limitations are in place. As a direct result, we see mods that are, in my mind, outrageous because they provide huge advantages, and players that have grown up playing with the appropriate arcade sticks are actually at a disadvantage. Of course, this rarely makes huge waves because mental skill will almost always trump technical ability, but that doesn't make the mods any more "okay" to allow. The example I used earlier in this thread was the Hitbox controller which allows players to easily "piano" 4 keys to achieve the same effect as a 360 degree stick motion.
As far as wear and tear, I've never really seen or used a controller where normal wear has had any significant effect on the controller. GameCube controllers are beasts in that aspect. The little bit of wear there is such as on spring resistance are things I would consider not ideal, but impossible to make a ruling on (not unlike your section about disabling light shielding which was 100% spot on and a big reason I have never pressed the issue when it comes to spring removal). Just to end this post with some semblance of a conclusion, we have already allowed a few types of mods to become popular, and none have any notable effects on gameplay (with the exception of trigger tricking which is frankly unavoidable due to in-game controller resets).
All I want to do is have our community draw a line in the sand so that people know what types of mods are allowable and which are not. Once we have an established standard, THEN we can have a discussion about expanding it to include custom notches or contracting it to exclude spring removal, but we are currently in a state of anarchy where
no one even knows what is legal. I'd hope that at most locals, if you show up to play with a fight stick, they would say that controller isn't legal, but I'd be surprised if there weren't a few TOs who would say go for it because they either don't care or don't understand the effect that ruling has on competition. The worst part is if and when it happens, the first player to complain he's fighting an uphill battle will be told "you can just go make your own fightstick!", totally missing the core issue with allowing mods.