I don't think we will know whether mods or popularity of mods is an actual indication of anything until the majority of the playerbase is participating in those things. Right now players who play mods are a minority faction of the player base and players who author mods are a smaller minority and players who author overhaul mods are extremely tiny. If there was no barrier at all to modding or playing mods so that everyone could do it we would likely have so many variants on the default version so as to see there really is no consensus at all about "fixing" anything.
Options are a good place to look for "voting". If 95% of the playerbase always adjusts their options to play 75% loot or less then that is a powerful vote that something is wrong with the loot balance. If 95% of the playerbase always enables feral sense every time they play then that is a strong vote to the devs for what the default version should be. Options are easy for everyone to participate in.
Just because a mod is popular among those who play mods doesn't make it a strong vote that the default version of the game needs to be changed in that direction. I also don't know at what point the devs would want to change a popular options to just being the default version of the game. If 90% 80% 70% of the playerbase always defaults to that option? What is the cut off point where that option would be viewed as a "fix" for the current default version? And if it is tough to know for such a clearcut action that is universally accessible like enabling an option then how much tougher is it to determine that based on authoring or playing a mod?
In the example brought up in this thread, item degradation is a very polarizing idea. I'm all for it but others would see it as breaking the game instead of fixing the game. If TFP ever adds an option for item degradation it would be interesting to see what percentage of the player base actually votes that the lack of it currently is something that is broken and needs fixing.