Hi,
Personally I create a custom-post-types.php file in the app folder, where I place the cpt declaration (using the johnbillion/extended-cpts plugin syntax)
In order to have the custom-post-types.php loaded, I am changing the “Sage required files” in functions php ( line 61 for me ) :
['helpers', 'setup', 'filters', 'admin', 'custom-post-types', 'acf']
As you can see, I’m also doing it for acf 