I have some agreement, and some disagreement.
For the most part, I take the direct incorporation of runes into the rules as a good thing. But thats because I don't see them as a statement about the direct truth of Glorantha, more nods to a bigger truth about it. The runes we show in the game are an abstraction, like all rules. We represent a persons entire physical body by 5 attributes (plus a few skills maybe) in RQ, and an arbitrary number (but probably less than 5) in HQ, and we know that in both games, these are abstractions that represent a very simplified version of the amazing variety of physical capacity that real people have. Every so often, we realise that these abstractions are inadequate to represent the range of things we know happen in reality, and we need to add something to them (eg we realise that, say, a specific injury like losing an eye or some toes, matters but can't be summarised with an attribute loss, or that it would be nice to have a way to distinguish between someone whose SIZ comes from being fat and bulky vs skinny and tall), and we all kind of understand that this is just the limits of abstraction and there are pros and cons to how we represent things in the game, and understand that trying to read big truths about how Glorantha works from physical stats is wrong.
I think the incorporation of runes into the game as a different kind of player attribute is a nod to a big truth about Glorantha - that everyones 'magical body' is different, and complex, and there are a whole bunch of things about your drives and world view and deep nature and connections to the magical currents of the world in there. This is a change from RQ1, but I think represents an evolution not a break. That you are limited to three runes in HQ (or that your magical nature is expressed in that particular rune system) is not so much a statement about Gloranthan reality, but a statement about how we might best represent that complexity to suit the needs of HQ. The new RuneQuest will represent the same thing in broadly similar, but more detailed, ways to suit the needs of THAT game system. 13th Age In Glorantha will do it differently again. A non-Gloranthan magical game might use different runes, but similar ideas (look at Nephilim for an example).
I do think, however, that sometimes the Runic representation within the game system is taken as being significant, and that's problem. I dislike the Waha writeup in HQ:G a lot for this reason - it takes the lack of a Spirit Rune as being very significant, but I think that the lack of a Spirit Rune is a game abstraction that might disappear or appear very differently in another game system that operates at another level of abstraction.