The distance between scaffolds is about fear of collecting ice, I believe. Supposedly when snow gathers at the meeting point of branches it can thaw and freeze and ice expansion and cause physical damage to the trees, but I believe it is repeated in the literature out of habit. When I became very serious about growing fruit 30 years ago i studied commercial orchards around me and most trees had scaffolds that violated this old rule. Also if 3 or 4 branches are more than half the diameter of the trunk and emanate from near the same spot on it they can stunt the central leader so it loses dominance. If you are planning to grow a tier above that point you would be out of luck.
As far as your oversized branch, this is what happens when you are not attentive from the very first season to the shape you are seeking. A commercial grower would likely cut it off, perhaps leaving a short stub to encourage a bud to form a new branch. If the tree ended up a 2-branch open center they might live with it. You have the time to repeatedly cut it back during the growing season so it may be best to work with it and try to stunt its growth until other scaffolds catch up, unless you are confident that a smaller existing branch can take its place. Plums tend not to be as cooperative as apples in allowing you to force branching wherever you need it by scoring the trunk. With young apple trees it is even safe to start over again and cut a trunk below existing branches because it will send out new shoots from older wood.
The problem with oversized scaffolds is that their diameter represents the amount of access they have to nutrients and water so they will fight you against submission to a less dominant role. However, they also need the energy from their leaves to stay in the fight and, if you are persistent, you can achieve balance.
Oversized branches also often outgrow surrounding tissue from the trunk that helps hold their weight, sometimes to the point of causing inverted tissue where it is attached there. Branches with inverted bark are the most likely to break and tear off the trunk when stressed with heavy crops or the weight of snow.