I want to create a new theme, but creating a new theme in Customization>Theme has limitations for working on DB, classes, custom forms, and so on.
But in app development, you can overwrite the classes and the theme and you are free to work with everything.
Is it common way to create a theme using app development? what is your suggestion?

I am unaware of any designers creating applications just to create their themes. Most designers use the theme system to create their themes, however many designers use Designers Mode for this purpose.