I'm quite sad to see the votes being mostly "yes" as this seems like a rather bad idea due the to the consequences. I also really worry about, if not hate, the thought of a handful of people voting yes causing changes that affect far far more other people.
I also don't think it's just a matter of worrying about someone exploiting it, I'm not so worried about that as people will find a way if that's what they want regardless. Though making it easy with an ingame mechanic is something that can be argued against.
Regardless I'm more worried about this resulting in good or better runes being lost due to it stacking with lesser runes. People who don't know about it are going to have a bad time and lets face it the changelog for CM Patch is already so big chances are no one reads the whole thing when they decide to try it just like people don't read EULAs, at most some people might read the most recent changes. This does not make them unreasonable, it's just the way people are especially with something called a patch rather than a modification.
Also as someone who would know about it I don't want to have to compare items on the ground to ones in the inventory any more than absolutely necessary. It sounds like it's going to be an annoyance while breaking the pace of things to make sure I'm not losing something. I can see it getting really frustrating having to check the inventory and compare things every time a rune drops, this could get more than just annoying.
I'm not aware of what limitations you may have with the alterations you can make with CM Patch though there are many better ways to handle something like this, and if those limitations mean this is the only way you can handle it then it's far better left alone.
If such a change is implemented it should be optional and opt-in, that way people who don't know about it don't suddenly start losing better runes and people who don't want to be annoyed with more inventory-comparing don't have to be. (the way the Morrowind Code Patch handles such options is a decent example)
There are already mods that basically allow more inventory space and I also think this falls more into the "mod" category than "patch" so all the more reason to make it an opt-in optional. This is beyond the purview of a "patch", this is not fixing something, this is an alteration based on personal preference.
There are many community/user made patches for many games, and it's very unfortunate when they start taking liberties with the changes they make while calling themselves a "patch". It's a slippery slope when a Patch starts taking to many liberties with the alterations made, some have even become hated due to such behavior which is a shame. So I suggest caution when adding such "mod" like alterations to something called a "patch", both for the sake of fans and the project itself.