Yes there is difference between both, which option to choose depends on your requirement. Below might help you in understanding the concept.
App Catalog Site collection is created for a single web application. You can consider this as Play Store/App Store for this particular web application. Now when a APP is uploaded to app catalog site collection. This APP is available for installation to every site collection created under this web application. So here usability factor comes in to picture. If your app is designed/developed to be reusable across all the site collection you can add your app to app catalog site collection so that other site collection admins can utilize this app for said business requirement.
Now when you upload a APP to particular site collection and NOT in catalog, this APP would be only available to install on said site collection. Other site collections will not be able to see this APP and cannot install on other site collection.
So it is up to development team to decide where to upload APP based on the functionality app is providing and if it is can be reused across other site collection.
Hope this make sense...