Generally because it’s nonsense. You don’t have redundancy in your cornea, and installing a diamond cornea doesn’t eliminate that non-existent redundancy. Same with replacing your stomach with three stomachs, or any number of other CBM changes. There’s a potential argument where CBMs act as immunosuppressants, but that becomes a bizarre nightmare of balancing and diseases are a pretty un-fun chore as it is. It could also reduce healing rate, but that’s another just un-fun annoyance rather than a serious game changer. Another option along that route might be to reduce the expressiveness of good mutations (i.e., someone CBM’d to the gills would almost certainly roll bad mutations), but that only works one way, has the same balancing issues, and is easily min/maxed by mutating before installing most CBMs.
And none of those really address the core issue of certain must-have CBMs being ‘must-have’. It would probably be better to reframe the question, since people are talking about managing the pile of CBMs they have installed. I’d look at it like this: if you, with no CBMs, and no mutations, found an Uncanny Dodge CBM (or whatever your personal favorite CBM is), what questions would go into your decision to install it or not? Right now, the only element that factors is the installation chance. Max HP cost, volume or weight management, immunosuppression, whatever, all just are drawbacks that you have to mitigate (and are easily min/maxed). Compare it to if you stumbled across a stash of Alpha serum. Your decision isn’t just based on the risks of injecting it, but also based on what mutation branches you’re closing forever to yourself if you gun for the Alpha threshold.