See, that explanation actually violates my SoD more than just handwavey "extradimensional organ", since a small extremely-hard-to-detect-yet-fully-represented-in-our-three-dimensions biological organ responsible for magic bullshit is just, well, hard to justify my belief in.
There's a reason why technobabble works - it allows you to invoke SoD yet defy current understandings of science. After all, "extradimensional" (or rather "multi-dimensional") is that working technobabble that applies to parahuman powers, plus that implied hidden dimensional connection to a massive fragment of a titanic being.
I actually prefer just side-stepping the problem of what a Linker Core actually is. The more you try to specify what it is in real world terms, the more risk you have of triggering someone's sense of realism. It should only really be elaborated on if it's important to the plot or for establishing internal consistency in a setting (e.g. in crossovers between MGLN and another universe that also has magic).