Confirmed, create company module with model override to extend the function you’ve modified in app/code/local/Mage/*. Use this company module instead of copying the whole file to app/code/local/Mage/*. This allows you to rewrite just the function that’s been changed, instead of rewriting the whole model, . On the next upgrade, you’re home free unless that function has changed.
This all works except in app/code/local/Mage/Core/* as core is the heart of Mage app and your modules won’t override anything in it.
Typically on the Store.php model the function roundPrice() has been modifed to round to 3 or 4 decimals instead of 2 for reducing sales tax round errors.
For anything in Mage/Core/ you will have to keep track of the changes and rewrite the php files every time you do an upgrade.