Sword of Spirit
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You know, I suppose an alternate option that also avoids giving free skills, is to just entirely remove the option to take a skill, and then leave the other options flexible. So anyone can use it for a combination of specialties, languages, and tools, but nobody gets a new skill out of it.I agree there are issues. I suspect the designers thought that giving up to five extra skill proficiencies to a high int wizard was too much, and would step on the bard's toes. The idea of giving specialisations instead meant that the wizard could still be a font of knowledge, but in a more focused, PhD kind of way.
Of course, with the rule in place, they needed to account for the possibility of characters without any knowledge skill proficiencies. And that is where the strangeness arose.