You're right, that didn't come across well. Let me try again
If the underlying assumptions are that any party capable of facing a CR 'X' opponent has access to magic weapons, then adding DR5/magic to many/most critters at that CR isn't a big deal. The party can deal with it, right? However, someone running a low magic or low magic item campaign will have to tweak those monsters, adjust its CR, maybe beef it up in other ways, to accomodate the fact that his players won't be able to bypass it's DR.
There's nothing wrong with this. But the more of those assumptions there are and the more you tighten the variation of any given CR (eg, somethings are easy CR8s, some are hard CR2s, etc), the more tweaking needs to be done. The more the published material zeros in on that ideal target (for those base assumptions), the less appealing the product is to those who prefer to vary from those assumptions.