Hey Kayleen, thanks for being super specific about what you were looking at, it was really helpful!
Yes, molecular geometry focuses on the atoms. I think that the diagram here just has the electrons on wedge/dash to remind us of the fact that these electrons are still taking up space around the central atom in a similar fashion which would give rise to our trigonal pyramidal vs. bent configurations we see.
I hope that that explains it. Let me know if you have any further questions.
Happy studying,
Molly