In my case, they never asked for proof of the flight booking and accommodation booking, I just wrote that information on the eVISA online application. Though I did book a flight and accommodation, I suppose that I could have still been approved by not making those bookings and just made up the information
Unless you really have to apply in Japan, I wouldn't recommend it. From seeing other people's experiences, it seems way easier and quicker to do it in south east asian countries