What's the most efficient way to get D8 to notice changes to .yml files?
In your development.services.yml file turn twig cache off and debug true. This will assist in theming, twig files are also cached.

Secondly, I think the command you want for yml changes is drush cr. However if they are install yml files, (I believe) they'd only register when a theme is enabled/uninstalled like modules are. So if that's the case you'd need to do that. I've also needed to use cr with libraries.yml changes.

Third, what VM are you using? I can run drush cr and it only takes ~5 seconds on the DrupalVM stack.