The main meaning is “to go under” which matches もぐる fine, no?
You’re right, I didn’t parse the explanation correctly, thought that もぐる is “to dive underwater or to go underground” and “くぐる” is “to go under or to pass through” while apparently it’s:
- もぐる - to go under, to go underground, to dive underwater
- くぐる - to pass through
Is it?
Basically. Although くぐる can also mean dive underwater.
Reading thought the definition on jisho.org seems it’s more like:
- もぐる - to dive underwater
- くぐる - to go under, to go underground, to pass through
Pretty confusing 
WaniKani doesn’t have all the definitions listed that Jisho does, but Jisho looks like it covers everything for both words to me. For instance, there are many more meanings listed for もぐる on Jisho than just dive underwater.
Consulted other dictionaries and it seems like:
- もぐる - the primary meaning is related to “diving”, the secondary to “going under”,
- くぐる - the primary meaning is related to “going under” and “passing through”, the secondary to “diving”.
Personally, I kind of like “to go under” as the main meaning, because it basically covers every actual meaning of もぐる.
“To dive underwater” is the first listed meaning in the dictionary, yes, but that English phrase only covers that one meaning.
“To go under” is a thing you can possibly say to describe going underwater, but you can’t say “to dive underwater” to describe, for instance, hiding under a desk.
So I kind of like that it works for any of もぐる’s meanings.
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