1-When using default jetways, and automatic mode selected, asking for jetway before asking for boarding will break the automatic sequence?
Only if you use a 3rd party airport with its own SODE jetways and you use the SODE menu to operate them, since the by-directional communication of the jetway status between SODE-created jetways is not yet available in SODE, so it will require a SODE update.
This should work if you always use the GSX menu to operate jetways, even at 3rd party airports with SODE jetways.
2-Another thing is regarding engines start at gate when APU is not available. In this case using Maddog X.
What I do is asking for pushback before starting engines. Otherwise, GSX won't work with engines running.
That's precisely the reason for GSX having the option to do a pushback before start: to handle the cause of an unavailable APU.
I have no time for the whole sequence of starting engine and disconnecting all the ground equipment before dispatcher asks me to release parking brakes several times. Is there any way that this won't happen until I am really prepared to push?
Just increase the delay time between messages in the GSX option, so the dispatcher won't call you as often.