Entra Enterprise apps and App registrations - Global Secure Access - Conditional Access Block

I am working on a rollout for Global Secure Access and ran into an issue with Entra Enterprise apps setup in the tenant. With Global Secure Access I have a Conditional Access Policy set to Block access to All Resources excluding some resources like Intune and Defender tap required for mobile setup.

When I added an administrator account which had done some Enterprise application setup and authorization for various third-party applications, those third-party applications stopped working with failed logins indicating token access issues. Upon review I found the majority of applications to be using client secret authentication with this administrator account as the authorizer. My limited knowledge of Enterprise apps leads me to believe this client secret is an application password that the third-party uses to keep generating tokens based on the authorizing account.

My questions surrounding this setup and further understanding are mainly in relation to how Enterprise apps and app registrations authenticate, as well as user authentication directly.

1. How does the token authorization work? Does the application just use the client secret to authenticate as the user who authorized it to generate an access token? Why does MFA requirements and changing passwords not affect this but specific Block policy does?

2. What are best practices in relation to authorizing third-party applications? My thoughts are a dedicated account to authorize applications when needed.

3. How will this work with applications regular users use? Say a user has a digital notebook that syncs with their OneNote or a calendar app that syncs calendars between Outlook and their website. Do these applications also use client secrets with the user's token and will break when added to the GSA setup I have? Is the only way around this to authorize with an admin account for token issuance?

Thank you for your time reading this and any insight you may have for any of the questions or ideas mentioned.