Ebike motor systems do not have a mechanism to recharge the battery - the motor is set up to only operate as a motor
so - yes - I presume it will generate some charge as a generator and motor are similar - but what charge there is is not going anywhere anyway
and ebikes are perfectly OK running with no battery
so using it in this way will not cause any problems with the ebike systems
as far as the 'smart trainer' is concerned then I can;t see why it makes any difference to the system at all - how can it tell??
Unless, of course, it is very 'smart' and you need to tell it what make and model of bike you are using it with - although I don;t know if any work that way (or why they would???) and you could always lie to it
Clearly, if it is connected to an on-line system so you can ride with others then there would be a possibility of 'some people' using this concept to look good and get fast times and KOM (QOM) and all that - but the OP says it will not be used that way - so I don;t see a problem.