Unfortunately it's not that straight forward. I've tested many of these apps, and the crux of the situation seems to be this:

If an application using NFC is in the foreground, the system only complains about an empty tag. But if the tag has for example text or other content, it doesn't complain that the tag couldn't be handled. However, if there is no application in the foreground that handles NFC, it will complain about not being able to handle the tag.

It can be easily reproduced even with ProfileMatic. If you're collecting tags in the NFC condition page, only empty tags raise the message. Tags that have, for example, Text record do not raise the message.

Now the problem of course is that ProfileMatic's daemon is never in the foreground. So even as it can handle the tag, system will raise the message.

It begins to look like the ugly hack of installing a dummy handler for some tag type (Text maybe?) is the only solution.