Hey there!
Can you provide details as to what cache is cleared when using the ‘Clear Cache and redeploy site’?
What does "Clear cache and deploy site" do specifically? 
What are the differences between a build that is triggered from a commit to the repository vs a build hook or the ‘Retry Deploy’ button?
Not a lot. We’ll build the files referenced in the commit SHA. So, for a re-deploy, that’ll be the last commit SHA. For a commit to the repo, we’ll likely get a later commit SHA.
The question I would be asking is – have the changes been made within the repo before the webhook is being called?