The plugin doesn’t remove the disabled sizes from the registered sizes array. Because it would be ambiguous. The plugin disables the disabled sizes just before creating the corresponding sub-sizes.
The plugin uses the right hook. so, if there is a plugin generates the disabled sizes, It means that plugin doesn’t use the right hooks or the wordpress core way for creating sub-sizes.
I would add an option for the user to check in order to hide the disabled sizes from registered sizes. but I don’t see it a good option, because it would indicate that these sizes don’t even exist which is wrong.