The most I have seen that is rather the functionality not being available in matter (ie the standard does not support it) so they are only available on zigbee with the manufacturers app.

No, it's also used for remote access, see e.g. Nuki and Tado.

Not super-nefarious, but this is probably just the beginning. If companies can gather data they will and if manufacturers can add features that require subscriptions, they will. The line always has to go up and Thread offers them the means to do so. If you give the opportunity, this always happens (see e.g. TVs, 'owning the glass').

Was exactly as fragile and dependent on manufacturer infrastructure for some fratures as you describe MoT.

I have over 50 Zigbee devices and never have a single issue (using HA and zigbee2mqtt, some on a separate Hue network). The Matter over Thread devices that I have, regularly drop off the network (no interference, etc., they just still seem very buggy). This also makes complete sense, since Thread adds a lot of complexity (IPv6, TREL, communication between border routers, etc.).