I think you have misinterpreted the rules a bit. Campaigning and party activity are prohibited with government resources.
The President and Cabinet sending emails on implementing political goals are permitted activities. Sending emails about ?NC platform discussions are not permitted.
When I went through ethics training with the GC, it was very clear what was and was not permissible. From the GC point of view, the default was use goverment email and save every email.
I can see the desire, particularly at the executive level, not to leave a record because policy formulation can be a messy activity. However, I'm not sure that is the motivation in this case. First, there is no control over the retention of the other end and, second, a lot discussion happens on the classified side.