To be fair, in real life, I usually see it used as a straight synonym for "understand" or "comprehend", just with extra geekiness. Very rarely is its special meaning actually intended.
Much more common is “expert” or “mastery” for that level of understanding, when I hear “grok” it means they read the Wikipedia page or did the tutorial or something.
grok: "understand (something) intuitively or by empathy; [no object] empathize or communicate sympathetically, establish a rapport"
comprehend: "grasp mentally; understand"