Admin has stated that sets containing players/individuals from multiple sports or categories should be listed under the classification that they are marketed as. Allen & Ginter is marketed and recognized as a baseball release, so there it should stay.
Upper Deck Goodwin Champions, on the other hand, is marketed and recognized as a multi-sport release, hence its classification under Multi-Sport.
As far as the OP question, it sounds like it should be one multi-sport checklist if they are all continuously numbered. But links would be beneficial
I'll never quit collecting entirely, but I am downsizing. Check out my COMC store and help me thin out what I don't want so I can buy cards that I do want. See something you like? Send me a message on here, and we can knock the price down quite a bit. I'll even take a bit of a loss if it means getting you a card you really want.