Normal 2 engine take-off, at positive rate gear up and flaps up. Select FLCH which will command auto throttles to go from V2 to 200kts
I'm surprised that there is no "speed check" included before retracting the flaps!
Gulfstream say almost the same thing in the G4, at VFS (minimum) select FLCH.
So if you want to look at things in isolation, there is nothing stopping you are per the manufacturers procedures from retracting the flaps at V2+X and 100 feet. This is exactly the way that you wanted. However if we dont look at things in isolation and the nice "FED" shows up and asks you how you are going to comply with the regulation pertaining to clearing all obstacles in the takeoff flight path, the only way that you can prove it is to refer to the manufacturers AFM (or software), this is based on the certification requirements of FAR 25 with a define profile where 400 feet is stated, so you would have to be able to show that you were in compliance with those procedures.
If FSI teach you the procedures in isolation, then they have just shouldered the legal responsibility for you flying into a mountain.
Mutt