There is some good advice on proper checklist usage in the answers given. Like FAA and civilian aircraft manufacturers, the military preaches disciplined and proper usage of checklists.
For the sake of thoughtful discussion, I am going to take a different angle on this and answer NO to the question of the pilot being reprimanded. Read on for explanation...)
There are actually several questions here, and multiple layers to each: e.g.
- Is it an emergency, or not?
- Is it a simulator checkride, or a flight?
- Is the deviation habitual, (i.e. something the pilot has rationalized to self and does regularly) or a one-time mistake?
- And what do you mean by “reprimand”?
First, in an emergency the pilot may deviate from any procedure to the extent required to deal with the emergency. In fact, complex scenarios involving multiple system failures are regularly encountered during simulator events to emphasize the importance of sound systems knowledge and ability to run multiple checklists, which may entail performing operations out of order.
Next, detectability. As mentioned, during a simulator checkride is it highly likely that checklists may need to be combined and/or run out of order during compound emergencies. It is also expected that during a busy situation some mistakes may be made, and that the evaluator will be aware of any deviation. However, during normal operations nobody will ever know. A majority of fighters are single seat, and the ones that aren’t are typically tandem, so nobody is actually watching the pilot as they run their checklists once initial in-type flight training is complete.
Next, intent. As mentioned above, a one-time, accidental deviation that has no consequences will go unnoticed, and a mistake may be forgiven, so I will assume from your question that the pilot has made a conscious decision to regularly perform a certain operation out of order. Also, that someone else – somehow - becomes aware of it and challenges the pilot on the practice. Even this has multiple layers though because some checklists are more important than others. For example, in the pre-electrical power checklist you are just sweeping the cockpit to make sure switches are in the right place. If the pilot tells the examiner that they flip one out of order because they are left handed, the flow makes more sense, etc. the examiner will probably just let it go. However, a deviation from a “major checklist” like the landing checklist would definitely generate some discussion, which leads us to...
Reprimand. Despite the perceptions of many who haven’t served, the military isn’t quite as rigid as it might seem. Aircraft type communities “own” their operating manuals and checklists, and treat them as living, working documents. There is generally an open safety culture that encourages communication and continuous improvement via the submission of change requests. If the pilot had a valid and articulate reason for their particular personal technique they might be encouraged to submit it to the model manager for consideration. However, until the change is approved they would be corrected by the check airman, and expected to comply. Ongoing willful non-compliance would likely be punished.
Therefore, given the condition that “it makes no difference”, my general answer is NO, a fighter pilot will NOT be reprimanded for performing a step out of order. However, he/she will be expected to comply with normal procedures and demonstrate proper checklist usage during any kind training or evaluation flight or simulator.