+ AA6YQ comments below
I understand your position, but under my point of view this is a functional limitation for Commander because I use my radio remotely, so it's very important to have control of all parameters.
+ The publicly released version of Commander can control all of a radio's CAT-accessible parameters via user-defined command sequences and user-defined sliders.
Your suggestion could be a workaround, but some radios, as Yaesu, store different settings for each operative mode, so it's ok on startup, but lost sync when the mode is changed.
+ You can create user-defined command sequences that issue mode change commands and then configure the remote radio for optimal operation in that mode.
Maybe you can consider to use the hamlib libraries, instead of develop your own code, in this case the radio communication is transparent and independent of radio model, so you could focus on your software.
+ Please point me at the documentation of the hamlib API that controls the notch filter bandwidth of every transceiver with a CAT-controllable notch filter.