This is most likely due to developers of certain apps/inputs and not iOS/Apple themselves, there is a simple line of code to do this and from what I've noticed some overly-secure-wannabe-apps force system keyboard for certain inputs.
Yes, developers can disable third party keyboards throughout their entire app with an application delegate method[0], and when secureTextEntry[1] is enabled on UITextField the system automatically disables third party keyboards on both that text field as well as any immediately adjacent text field (likely for username+password combos).
The idea is that because keyboards can connect to the internet (with user permission), there's potential for data theft. It may also be possible to exfiltrate data from a keyboard extension by saving the data to an app container shared by the host app, which the host app can then send out with its network access.
Devs who don't know how or care to properly accommodate the variable height of third-party keyboards may use the app-wide opt-out to eliminate bugs relating to that, though I haven't personally encountered this.
