Whatever you tell your manager, stay away from the approach you used in this letter. If you meet with him and use language laced with resentment and prerogatives, you are likely to cause your manager to think more about his prerogatives in this matter.
You indicate that as a salaried person, you can take as long a lunch as you like, but you left off an important addendum, namely "within reason." If your lunches last for hours and they are not actual business lunches, then you have stepped out of the reasonable range. As a salaried individual, it is expected that in return for your autonomy, your actions will be professional, honest, and businesslike.
The larger issue is that this feedback from your manager may indicate that he is dissatisfied with more than your lunch breaks. This is a good time for you to take an honest look at your performance and the hours you are spending at lunch, and then make adjustments if warranted. If you still want to discuss this matter with your manager, concentrate on business-related reasons behind your long lunches. For example, if you work excessive hours every day, or if you use these lunches as business meetings, that is worth discussing with him, even at a lunch meeting.
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