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.

I’ve never seen it used in that way, almost always it means to completely know something on a very deep level. To know it inside and out, etc.

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.