The trouble with devoting so much extra time to edge case migration features is that the time (in my opinion) is better spent adding features to the new version. I don't mean to sound harsh so please don't take it that way, and I realize the documentation is pretty extensive and there's a bit of a learning curve, but version 3.x does *way more* than 1.x with the only real loss at this time being a visual way to dictate which CPTs are enhanced.
Given that, we need to take a step back and look at what's changed in 3.x and see how that applies to what 1.x used to do: version 1.x applied the same meta box to any CPT you decided to support. Version 3.x now has a ton of custom attributes, and the ability to add multiple meta boxes. So I can't make a blanket decision to apply all of the settings everywhere because everyone's implementation is different.
The migration script is meant to be a one-time thing; many people choose to ignore all of the documentation, the tooltips, and the instructions during the migration itself. Once the data has been migrated it's in the new format, so opening the door for multiple migrations would result in a ton of data duplication (the migration script doesn't delete legacy data (on purpose)) so I don't think facilitating subsequent migrations is a wise use of time at this point either.
I completely get that extending existing plugins with Attachments might be a high percentage of use cases, and I do plan on elaborating the Settings screen itself to make things a bit easier to implement, but a lot comes down to custom instances which each have custom properties, and how the UI for choosing which instance goes with which CPT plays out is a pretty complicated matter. Leaving it all in the code forces implementations to be intentional as opposed to global, something I much prefer. It's not too difficult to determine what CPT name a plugin is using for it's functionality, so extending them should continue to be pretty trivial, as you've discovered. I don't mean to suggest that devs should rewrite every plugin they might want to use Attachments with, sorry it came across like that.
I truly appreciate your feedback and will definitely take it into consideration, but this is only the second request for CPTs in the settings screen and there are a number of things I'd like to focus on before that. I haven't had anyone request subsequent migrations either, but maybe I could put together a separate plugin that does just that (migrates a version 3.x instance to another version 3.x instance) and at the same time keeps it separate from the plugin itself. I'd love to get more feedback on that as other people might find it useful, but perhaps only after a borked migration attempt in the first place.