Never Mind, but in case anyone else runs into a similar problem, I discovered the underlying reason.
Turns out the template that I borrowed from a fellow HLO user has the Automatic Bonus Progression selected from the GMG Magic Item Variants section, and by doing so, it was hiding the Fundamental Rune choices.
I would like to add my 2 cents. I think inserting a message on the Fundamental Rune selection stating ABP is in effect, making fundamental runes unavailable communicates why such runes aren't selectable..
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