speaking of good practice, same for opening multiple issues about the same subject 
your duplicate: Rename src/app/
anyway I follow @anna_liebt have you try to modify your tsconfig.json ?
"include": [
"src/**/*.ts"
]
furthermore, if you read the README of Ionic app-script GitHub - ionic-team/ionic-app-scripts: App Build Scripts for Ionic Projects you will find an option ionic_src_dir respectively --srcDir in chapter Overriding Config Values