Vegetables – When cooking grains with vegetables, should I cook them together or separately

It is true that flavour is affected by cooking time. Most likely nutrients as well, but its about the vegetables. If you cook beef stock you should indeed cook it for several hours to release the collagen and proteins. My experience with chicken takes less time so 30 minutes in the pressure cooker or 1,5 hours in a normal pot. Then you can eat the meat as well. Vegetables should only cook for 30 minuts so add the vegetables 30 minutes before the end of cooking regardless of the kind of soup. The fresh flavor of the vegetables will disapear if you cook it for longer then that. Someone doing research on the flavour development and time for making stock

There's no reason why you couldn't boil vegetables as you make the stock and then puree them in as a base. It's really about taste and the result you want.

Making the stock without vegetables in it will give you a clear broth with a simple pork flavor and the vegetables will be distinct in it. If you add vegetables while cooking the stock and then puree them in your base will be much more vegetable-y, and opaque - the color will be determined by the vegetables added. The pork taste will be a bit more hidden by vegetable flavors.

Spices and herbs are 2 separate matters. In general you can overcook herbs very easily but it's hard to overcook spices (although some spices can change during long cooking times). Adding bay (laurel) is one of the exceptions herb-wise. Spice-wise adding at the beginning will make the spice permeate the meat, careful not to overdo it though.

Like I said it's all about the look and taste you want.