When I am receiving flight instruction from a military flight instructor in a military aircraft and I am not a military pilot (just have a private pilot certificate) and the instructor endorses my logbook to show training given is that allowed? Is this allowed per 61.41 sine the instructor is in a program designed to train pilots?
As you are aware, 61.41 allows you log military training but only as long as you are "in a program".
(a) A person may credit flight training toward the requirements of a pilot certificate or rating issued under this part, if that person received the training from:
(1) A flight instructor of an Armed Force in a program for training military pilots of either the United States or...
Whether or not your military flight instructors have FAA Flight Instructor Certificates is irrelevant as long as they are qualified by the military to teach you in the aircraft that you are flying, AND you are in a program for training military pilots.
If your friends are not FAA CFIs then they cannot give flight instruction in general aviation aircraft outside the military.
If they are, then they can.
It's really that simple, but you cannot randomly mix and match military and FAA flight instructor qualifications as your question seems to suggest.