Questions about toddlers and food are very common and I appreciate you asking. Most children move from breastfeeding or bottle-feeding to eating regular food with the family over a period of about 12 to 18 months. Most toddlers and families go through this transition fairly easily but sometimes there are some questions along the way. Your 16-month-old who is choking on food will most likely turn out to be fine but the issue you raise is worth thinking about.
My first question is about your son's overall development. If he is progressing in speech and socialization, then it is much less likely that the choking is a developmental problem. I would encourage you to discuss your son's development with your health care provider during his next checkup. It is also right to think about any medical causes of the choking. Your health care provider or dentist may want to take a close look at teeth, gums, tongue, and overall swallowing. Your provider might also want to look at the size of the tonsils and adenoids, and may ask about any signs of obstructive breathing during the day or night. If there are lingering questions it might be best to see a specialist. If everything checks out well, your son may just need more time. As a parent, you will need to continue to work with him. It will be important for him to sit while eating and for someone to be close by in case he has any more trouble. Good luck.