How can this be fixed without breaking existing software? Re-ordering the list?
Not sure how much of that is still around but it was rampant for many years and likely a key to Windows success in gaming.
Or, even simpler (and AFAIK modern Windows does that too): if the running application doesn't say in its application manifest "I'm a modern application which understands the new things from operating system versions A, B, C and features X, Y, Z", you know it's a legacy application and you can activate the relevant compatibility shims.
They just need to adapt the API to also filter the list of resolutions when the compatibility mode is on.