I might be wrong, but I think that if you inject your config file directly into the iND bios, then it should eliminate that loading screen because the loading screen is there to give the bios time to find your config file. I don't believe that there's a way to inject config files into the X2 50xx bioses. The reason that I recommend X2 5035 is because iND 5003's in-game reset feature is bugged in that it doesn't require you to hold the triggers in addition to pressing the face buttons to trigger the reset, which could conflict with the button mapping of some emulators, but if this doesn't bother you, then use iND 5003
Neither bios will actually set the clock to the correct time if that's what you're asking, but yes, X2 5035 does set the time. Both bioses will set the clock to an arbitrary time if it detects that the clock's not already set on bootup. It'll still be up to you to set it to the correct time. If the Xbox is connected to the internet, then you can use XBMC to automatically sync with a time server on bootup.