refactor: improve fetching repositories with custom properties

[PendaGTP]

Description

Related to: #740

This PR refactors how we fetch repositories with custom properties.

Changes

• Replace manual endpoint construction (github.request.endpoint) with the built-in github.repos.getCustomPropertiesValues
• Standardize pagination to 100 items per page to match other API calls
• Improve error handling
• Simplify nested loops and improve code readability

Testing Done

Ensured all unit tests pass.

[HagegeR]

FYI:

safe-settings/lib/settings.js

Line 485 in 3b7eb05

const existingRepoResults = await github.paginate('GET /installation/repositories')

also does not leverage the 100 results per page

[PendaGTP]

@HagegeR

I've also noticed there are other GH API calls in our codebase that don't use the per_page parameter. While this PR focuses specifically on improving how we fetch repositories with custom properties and making that process more readable, I've also included the per_page parameter as an initial step toward addressing issue #740.

I suggest creating a separate PR to comprehensively refactor all GH API calls for consistency and performance.