You're right, the debug layer does not notify you of all transition issues yet, so the fact that it doesn't complain about things doesn't mean that your code is correct. Expect these issues to turn into errors at some point in time.

There's not a lot of hand holding in D3D12, make sure to do your research and cover all cases.

If the debug runtime doesn't complain, does it just not matter?

There are going to be cases where the debug layer cannot infer incorrect usage of barriers since it cannot know at record time what the state of the resource will be when the command list is eventually executed.

If a command list contains a single transition barrier from Render Target to Shader Resource, that's fine. However, to execute two such command lists in sequence would result in invalidly attempting to transition from Render Target to Shader Resource twice. The resource would already be in the Shader Resource State after execution of the first command list. Nothing was incorrectly recorded at draw time that the debug layer could alert you to, it's only at Execute time that this could possibly be detected.

Nothing was incorrectly recorded at draw time that the debug layer could alert you to, it's only at Execute time that this could possibly be detected.