1. The change is the more correct system operation than previous. It is also not immediate. The nav system is aligned, but the attitude alignment is not. The path is supposed to be there, this was a bug that has been rectified. So, no, your assumption is what is 'more real' and what is not is incorrect.
2. The logic flip has to do with MP sync issues, so at this point, the default will be fast alignment with the option for full. And its also false that it should have no alignment, it will save previous values from the prior 'simulated' sortie.
3. The alert status option is a holdover and does not really accomplish anything at the moment, or shouldn't. My hope is that the devs apply that to alert switch positions, but its not going to be a high priority if they choose to listen to me and apply that, so it will likely be a down the road thing.