Matter is not a transport layer. We talk about "Matter over Thread" or "Matter over WiFi". Matter is an application layer that is sent over some kind of transport. This new thing "Aliro" seems to be another application layer used for a different purpose from Matter. Aliro is for exchanging encryption access controls between devices.
An analogy would be that "HTTPS" is an application layer for sending web pages over some kind of transport layer like WiFi or Ethernet. "SMPT" is an application layer for sending emails over some transport. One should NEVER ask why SMTP is not part of HTTPS.
Another analogy is that railroad tracks are a standard. They all have the same width and so on. But there are tanker cars, passenger cars, and box cars. All these standard cars can run on the same rails. So now we have HTTPS, SMTP, Mater, and Aliro that all can run on the same WiFi or whatever transport standard. All these standards are layers that stack.
Note: Yes, I simplified this and "bent" some terms. For a better understanding read this:
https://en.wikipedia.org/wiki/OSI_model