Since v2021, almost all the generated pages use MVC (Model-View-Controller) approach; including Custom Files (especially with "Include common files" option enabled).
1. Please provide the area inside the project separately, to write the code that will be generated into the *.php files in "models" and "views" folders.
In the existing condition, there is only one area to write the code that will be generated into the *.php files in "views" folder; it is from "Custom Templates" -> "Table-Specific" -> "Custom File" -> "Content".
Unfortunately, we cannot customize the generated code in *.php file that will be put into "models" folder.
Most of the time, we had to customize the code in the generated .php file in "models" folder, especially for the PHP code that runs the db calls, Ajax calls, etc. We cannot combine this code into the *.php custom file in the "views" folder.
2. When we double click the Custom File from "Database" pane, then it should be open the code area, since Custom File does not have Table/Fields setup.
The existing condition, when we double click on it, then it will not open the code area to write the code, and this looks not very user-friendly for us.