When I go to System -> Configuration -> Catalog -> Inventory -> Product Stock Options, Limit Maximum Qty appears under Default, but not when I change to a specific store scope. Is there a way to set this limit on a store/website level? Or do I have to set this option specifically on all products using Update Attributes in the Catalog Product admin view? I would prefer to still use the config option if possible, as it doesn't involve a large query to the database.
Yes technically it is possible to set-up this system config value to be on a different level. The code itself is not so complex you just need to override the values in the system config, using your own module ideally and not changing the core code.
<show_in_default>1</show_in_default> <show_in_website>1</show_in_website> <show_in_store>1</show_in_store>
But I am never sure about changing these sort of things, as often they are done for a reason. I would always suggest a large amount of testing when changing these sort of things in Magento and to be honest would possibly suggest sticking with the per product solution.