I completely agree with your doctor. I would stick to your guns. Don't make him something separate that you know he likes just to get him to eat. He sounds really stubborn, but if he gets hungry enough, he will eat.
I am not sure how you set up your dinners, if you bring all the food to the table or fill the plates before coming to the table, but have you ever tried letting him "fill" or scoop his own food on his plate?
Being "full" is a concept that young kids have a hard time understanding. I try to make sure that if my son wants "extra" of something, it is not until his fruit/vegetable are finished, that way he isn't just eating all carbs. If he eats his spaghetti first and it is gone, he needs to eat his green beans and oranges before he can have more pasta (that was the case at lunch today) and he ate most of his green beans and said he was done. I couldn't tell if he had eaten any oranges, so I made him eat 2 pieces (because he is 2 years old and I wanted to make sure he got a "taste" of the oranges).
There are going to be times when your son doesn't eat much - if he is getting sick, sick, or getting over being sick, growth spurt, tired, etc. There will be times when your son eats everything in sight!
Maybe having your son help cook would help him get interested in his food, too. My son LOVES helping to cook, dump in ingredients, stir, bake, etc. It takes a LOT of supervision, but it is fun to get them excited about preparing food as well as eating it.
If he did not finish his food, I would not do dinner treats. I wouldn't resort to "bribing". My husband and I have been known to save our son's dinner plate (if he really doesn't eat much) and if he says he is hungry before bed, out comes the dinner plate!!! :-)
Good luck! I babysit an 18mo old who is a VERY picky eater and it IS quite stressful!! I am SO glad our son is not picky - but being 2.5, he has his moments too! :-)