Yes, you can. I use helicopter mode on my radio for the same reason. I wanted the middle of the stick to be ‘softer’ by creating a throttle curve. In heli mode, the radio will automatically control two channels at the same time (throttle AND collective). As long as you only use the throttle channel and not plug anything going into the APM into the collective channel, things should work fine. This means you basically a lose a channel on your radio.
Yes, there is no technical reason you cannot use a Heli mode on the radio. The main reason we recommend against it is we have a lot of completely new users, who don’t know how to program a radio, so we like to keep it simple.
If you are an experienced user, you can use a Heli mode to benefit from it’s features. The only thing you MUST do is use an H1 swash setup, so that the pitch, roll and collective commands remain separate and not mixed in the radio.