It's not a question of overwriting. When the map loads, the #include lines are replaced with the contents of the specified .script files so that you get one giant merged script file in tdm_main.script. tdm_main.script includes tdm_custom_scripts.script, then tdm_user_addons.script, so the contained scripts will be added in that order.
If you #include the same .script file multiple times from different files, like in your example, you risk getting multiple copies of the same script which causes map loading to fail - see one-definition rule. Inclusion guards (#ifndef, #endif etc.) stop more than one copy of the same script from being added.
If you want your version of the script to take priority, you should give it the same file name and folder location as the base script, without using tdm_user_addons.script. It works the same as, for example, letting a custom model take priority over a base model.