I feel like I am chasing a red herring, so I'll ask the broad question. Have you ever experienced the "Show Role Differences" feature to not be accurate or detailed enough (aka not comparing everything)? I compared two roles and they match but in one of the roles, users cannot see all of the same records.

could be that the users' subsidiaries are different? or even their departments, if there are restrictions based on department etc

Tagging on to that, some access (depending on how it's setup) is not controlled/visible at the role level (e.g. custom records, custom fields, even custom forms sometimes)

yes, good call

Plus scripts or workflows could also be running that are hiding things

just throwing custom segments into the mix too

I experienced this with custom records like those relating to FAM.

Sadly spent 8 hours today going through each of these. Created a ticket with support in hopes of them helping. I'll post back next week if there are any updates.