The MySQL data folder and htdocs inside /Applications/MampStack.app/Resources/app are only used in the first boot of the application. At that point, they are moved to the sandbox directory (the directory provided by Apple in which the application have full access) under your home directory: ~/Library/Containers/com.bitnami.mampstack/Data/app
From that point, that is the folder used to the files requiring write permissions. Executable files and other read-only files are still used from /Applications/MampStack.app/Resources/app.
The data and htdocs from /Applications/MampStack.app/Resources/app will be also used if you delete ~/Library/Containers/com.bitnami.mampstack/Data/app. In that case, it will initialize again a fresh environment.