I think maybe the concern your Dr. has is that some children who stay on purees past one year of age have a higher risk of developing texture issues. Also fresh food is more nutritious then canned or jarred food whether it is baby food or not.
When DS started solids i just started offering him whole pieces of food to "eat" he started at 7 mons and he mostly squished, licked, nibbled and smeared the food. That's ok, I just kept offering it to him working our way up to 3 meals and 2-3 snacks a day (or so) Sometimes it can take 8-15 times of offering a new food to a child before they will eat it.
There are some great books out there, I am reading one now called The Toddler Bistro
which is really easy to read and gives lots of great info,some tips and some yummy easy recipes.
Also Dr. Sears has a good nutrition book
I think it is important to offer your son whole fresh foods and to get him used to all kinds of yummy fruits/veggies,grains, proteins, etc. Here are some tips I try to keep in mind when feeding DS.
1. A balanced diet for a toddler is not about every meal or even daily balanced but it tends to balance out over the week as long as a variety of healthy foods are offered.
2. Your job is to offer healthy foods and reasonable times through out the day your child will decide which foods and how much to eat from his plate.
3. When introducing a new food make it look appealing and present it in an attractive way (ex: a fruit slice rainbow)
4. Serve new food with at least one thing DS likes to eat. So if your DS likes the baby food bananas serve that in a dish with a little mini zucchini muffin and a bowl of frozen blueberries.
5. Try preparing the same food different ways (DS is not crazy about mashed sweet potato but will eat a whole sweet potato if I slice it into fries and back them.
6. Eat with DS, he would always eat more and be more interested in food when I was eating. he also would be more interested in trying new food that was off my plate.
After a year old I would offer DS his meal first and then his drink, incl breast milk or in your case formula.
I think a good plan for you and your son would be to offer breakfast while you eat, then offer a drink towards the end of the meal. The same for Lunch and Dinner. Also I wouldn't stress about him having 3 meals and snacks right away, you need to work up that that. I would also try to replace some of his formula with goat milk,you could also do some goat milk with his formula and just keep increasing the goat milk amount as you decrease the formula amount. Again this is gradual. As your LO's palate broadens and he starts really enjoying a variety if whole foods his bottle intake will decrease.
You are right to listen to your baby and to encourage him to listen to his body cues
. I just think you need some information on nutrition for toddlers. Check out the books mentioned above and here
is a great link from Dr. Sears.
Oh and DS loved "nibble trays" at a year old and still does.