Apart from Bloodhound, I can't think of any tools where we have graphs.
For web security, I can't think of something where "graph thinking" applies. But we have a pretty huge list of attacks to test https://portswigger.net/web-security/all-topics.
And ultimately, what is inside your pentest report ? Not a graph, a list of things to do:
- SMB signing.
- Don't use the domain admin to manage every machine.
- ...
The main reason this phrase is so popular, is that it panders to the hacker community: "We are the smart guys, all the defenders do is excel sheets."
IMHO, the nugget of truth in this is that defenders can spend considerable amounts of time on things that don't matter. Like doing CIS benchmark by hand on all servers. While missing the low-hanging fruits that would give them a strong security posture.
In a lot of companies, the defenders are just sysadmins that don't have any idea of what they should focus on.