If you stablished your device to work on three channels only, then it is ok to have all messages in all channels in LORAWAN FRAMES (Gateway window), and only those in the selected channels in the device windows.
I don`t see any problem here, you configured the system in a way and then the behaviour of the system is sequacious.
Please, make it clear which is your problem/question…
This is not possible. The same configuration will be applied to all devices (OTAA and ABP). If you set 8 factory channels in the device-profile, then ChirpStack will immediately send a mac-command to only enable the first three channels.
The information you enter in the device-profile are the boot parameters, e.g. the parameters that the APB device uses when it boots. If ChirpStack sees differences between the parameters used by the device and the configuration in the .toml file, then it will always bring the device in sync with the .toml file configured parameters.