I still have not found a satisfactory answer to how this effects "Thread" devices. I'm guessing it doesn't but I would still like to know more about it.
very very basic breakdown, but...
matter is a communication protocol, it's a language, it specifies how the devices format messages to each other over IP networks. it has a list of attributes devices can have, as well as how values for those attributes should be formatted.
thread is a wireless networking spec - think of it as "fancy" wifi, it just specifies how devices connect to each other using radios. It's IP based, so can handle the same packets your regular network can.
so devices should be able to "speak in matter" over thread
devices can also speak matter over Bluetooth, and wifi.
without matter, one device might call a parameter brightness, and go from 0-255, while another calls it dim level and goes from 0-100. so even though it's controlling the same physical attribute, the 2 devices don't know what the other is talking about. This more applies if one device is a light, and the other is a controller.
homekit is basically the same thing as matter, it just defines how the commands are formatted. but if you want to
depending on how the device manufactures decide to do it, devices will talk homekit and/or matter. Meanign they will be able to interpret both homekit and matter packets. Those packets can either be delivered over ethernet (wired or wifi), bluetooth, or thread.
the home app will be "bilingual" and talk both. and choose which to speak depending on the device it's trying to talk to.
my guess is more devices will migrate to matter, as it's open source, so you can just make a device speak matter, and it can receive commands from any controller.