if you restore from a fragmented paper wallet backup, you will enter the keys into the program, it will then ask you to verify the fragment ID is the same as the one on your paper. You won't miss it. And the fragment ID will always be different from the paper backup because now the fragment IDs are always random.
Hmm there may be some misconceptions here. Fragments have always carried 2 IDs: the wallet ID, and the fragment ID. The new fragment ID is random instead of derived from the secret, but there always was these 2 IDs on the paper fragments to begin with. Are you saying the fragment ID from old backups is off now?
When restoring fragments, the code presents you with the fragment ID to check against your fragments at first. Once enough fragments are provided and the secret is reconstructed, it then asks you to compare the resulting wallet ID with the wallet ID on the fragments, which they also carry. This is a 2 step verification that should make sense on its own.
Let me know if you there are specifics in the GUI that you believe are off.