From whom did you hear you had to wean him from the bottle 'soon'?
Really, a lot of the half-baked advice you'll be getting (and doubtless have been getting already) is nothing more than fear-mongering and invention.
1. Have you considered that what is waking him up is hunger? That would certainly explain why eating is what puts him back to sleep. I mean, if he needed to have some cold night air or some running around, the bottle wouldn't work, yeah?
2. Children should not drink unmodified cow's milk (or any other mammals' milk apart from their own mother's) until well past a year. It is tremendously high in sodium and calcium -- far too high for little kidneys to deal with when it is 1/2 or more of their daily intake of food. When the full mixed diet has replaced the bottle for all of his meals and most of his snacks, it will no longer be imperitive that he drink ONLY modified milk (formula).
3. When he is 5, he will not be waking in the night (not even out of 'habit') for food, and his need to fall asleep with food in his mouth will have gone away completely. Are you in a hurry, or is someone around you in a hurry for your lad to be 'already grown' on the dark suspicion that if you don't force him to get over being a baby, he won't?
What should you do? Carry on doing exactly what you're doing. It's working, no one is being traumatized or injured in any way. Don't fix what is not broken.
You may like to stop telling whoever is giving you this kind of advice what is really going on in your life, and answer all questions about feeding and sleep with 'we're doing fine, I'm so glad you asked.'