Sorry for the delayed response.
I cant say for the process you used to clone the card but I dont think the cloning process was only a partial clone. I have an assumption that your card, in the first 6 sectors, are using non-default keys; that is keys that are not commonly used when you get a new card from the factory. To elaborate more, the usual default key of a blank/non-provisioned card is usually FFFFFFFFFFFF (read: 12 hex bytes, all 0xF). TagInfo only has the default keys in the application thus if it uses non-default keys then TagInfo will show those sectors as unreadable with the note “unknown key”.
…it appears most chips come with a secured unalterable UID
This is accurate for non-magic cards hence the use of the word ‘magic’.
The ‘magic’ in these cards should be seen as additional features that aren’t available to their non-magic counterparts. For example, gen1a magic cards have an additional command set that bypasses any need for authentication (use of keys) to do any card operations (like read/write). However, since this is done by a special command set, its not easily done by a phone or generic encoder. This is why the proxmark is generally recommended to serve this purpose.
If you were to acquire a proxmark, Id be happy to help guide you through the processes of setting it up and some investigation into the Mifare cards you have, in addition to trying to clarify any questions/misc issues you are facing. Id be happy to walk you through the process of a cloning a MFC card so that you can offer that service in work by making duplicate tenant cards.