Ok, I hope I remember all the questions.
For one, tomatoes are packed in WATER and canned for the 40 min. So, unless you want to put water in them they will take longer than that other than crushed. The crushed tomatoes turn out well. I actually prefer that method now.
The reasons for the difference is part density or thickness of the food in the jars. Some is due to whether or not it is a hot or raw pack. The hot, crushed tomatoes is shorter due to this.
Soup directions are considering only half the jar is solids, half liquid. Again, packed hot and also the density will be different.
They are tested in the labs for these things, as well as ph, of course. They put probes and things in the jars when testing to determine these factors.
So, personally, if I were you, I would can it like chili con carne, but leave out the meat if you want it a bit thicker. If you want it soupy, then use the soup method and only fill half full of the fully rehydrated and cooked beans and other things. It is up to you, but it will depend upon the density.
The ground meat in the chili con carne will be a little less dense than all dried beans. Those beans swell, have a lot of starch, which take longer for heat to penetrate.
As for the vinegars, I have no real answer other than it is a final flavor and color issue. Processing would most likely make the color change. You can use real pretty bottles, seal with corks, and use colored sealing wax for flavored vinegars. You can put a piece of thin ribbon or cord in the center of the cork, tape the sides down, then dip in the wax. Then you have a pull string to peel the wax with. Real classy looking things. I have done these before for gifts.

AH ok. :) That totally makes sense. So the Chili con Carne recipe is for 75 minutes for pints because it is dense, and not because it has meat. I had just assumed meat required a longer processing time because it can have cooties.

It is both the ph level and the density. Yes, the dried beans will be more dense due to the starch in them.