Hi Paul,
You can have a standalone Apps Script file and it can still make changes and additions to any spreadsheet if you give it the right permissions.
Issue becomes more how you direct it to pick a particular Spreadsheet to modify.
The other question is whether you need particular triggers on that Spreadsheet like on Open, on edit or on change. If you need such triggers, there is no alternative but having some minimal script in the Spreadsheet container.
For changes to be effective across multiple spreadsheets, you can make the large bulk of your code into a library and then just invoke it from a very small script in the Spreadsheet.
So up it is to your situation and what you prefer doing.