I garnered that :
the OP is using words whose meaning are special to him and those definitions are not common to anyone else.
hate to sound so negative, but if you truly understand the meaning of the word, (this is fundamental to human intelligence ) if you truly understand the meaning of the words, you will understand the concept and your communication will be clear and concise.
a "programming environment" means something special to the OP. 'That' meaning is not shared with the rest of us.
what we do know :
he wants to overide the bootloader
he wants to use a standard bootloader
B) Arduino to Arduino programming.
III ) well, he is a little light on this point.
I know that others have created a 'sketch uploader' you take it to your pre-configured Arduino UNO, plug it in, and it uploads said sketch. a travelling programmer, but AFAIK, has a direct connection.
If you have an Arduino that is already running a program with a wireless device, you would have been able to put in some sort of program that could set the device into a state to accept the new program. as DrDeitrich says, create a bootloader that has the ability to be put into this mode.
I do think the receiving Arduino would have to have been pre-programmed to be able to be put into a state in order to accept a new sketch this way. you could not do this to a raw Arduino.
another way to do this is to use a second Arduino. have a pair on the receiving end. one is running, connected to the net, bluetooth, xbee or some such. and that chip downloads the sketch, then programs the second Arduino.
taking this last bit a little further. the ESP8266 is already a second micro. it might be possible to connect that to the target Arduino and then send the program to the 8266 for it to program the target.
In reading the post, and why I say this is an X/Y Problem is that he does not tell us what he wants to do.
he only tells us the STEPS he is having problems with.
does he want to create a master virus dispensing device that will 'find' any run-of-the-mill arduino and then program it to his program ? ie: standard bootloader. we all know this is impossible.
Does he teach a class and want to take each board each day and sit it in the programmer and have it wirelessly program the board for the day's lesson ?
Does he want to make a device for use, say a thermostat. some imbedded device, then offer a way to wirelessly upgrade the software ?
Is he involved in a battle of the robots and wants to perform Kirk's Kobayashi Maru manoeuvre ?
the REASON for doing this is not here, only the steps he wants to do. that is one of the fundamental tenets of an X/Y Problem.