The flighttime column isn't used internally anymore, only the flighttime_stamp. As long as the flighttime_stamp column is correct. I haven't removed that column yet, but I will be for the next version. But as of the previous version, it's not used anymore.
From the PIREPs it always comes as HH:MM:SS I believe. There's only a reformatting of a time if it's been typed in. Times are *not* stored as decimal as you indicated. It's always in HH:MM:SS format. If you're seeing decimal formatted time anywhere, then that's a bug. I'm not sure where else you got decimal time notation from.
It's in HH:MM:SS format to allow MySQL to do any time summations, and I don't have to handle that. It comes from ACARS as HH:MM:SS format as well.
During editing, if it's reverting to decimal format, then that's a bug.