It doesn’t seem like the tests and reagents are the same for all bacteria – what gives?

When you create an unknown, the software automatically loads in all tests and media appropriate to bacteria of that Gram reaction. So, the software will have different available tests, media, and reagents for Gram positive cocci than it does for Gram negative bacilli. This is not unlike the difference in the tests one would use in a wetlab for identifying bacteria from these two groups.