I figured the best way to write this out was in the form of some sub-par user stories.

As a Salesforce Admin, I need the ability to do a comparison of two orgs/repos and have it show only non-namespaced metadata so that I can easily distinguish between things I own and manage vs what are from managed packages.

As a salesforce Admin, I want to be able to indicate that I want to hide all namespaced metadata while still being able to show custom fields I create on a namespaced object so that I can quickly deploy new custom fields.

As a Salesforce Admin, I want to be able to quickly see my custom metadata without all of the white noise of managed packaged metadata so that I can make deployments quickly and accurately.

As a DevOps manager, I only want to manage things we have actual control of in our repository and not include name-spaced fields so that our repository is an accurate representation of the custom metadata we need to manage.

Acceptance Criteria:
Ability to indicate that the user only wants to compare non-namespaced custom metadata
Comparisons are able to manage custom metadata like fields that are on managed objects