I think your question is how to make by jig work for box joints. Sometimes the correct answer to to toss it and get something else. These type dovetail jigs do a good job of dovetails but are lousy at anything else. I have an I-Box from Incra and it makes flawless box joints. I also have a 25" Incra positioner that can make them but the I-Box is so simple and elegant. You have an initial adjustment but after it is set up you just put it on the table saw, adjust the blade height and bam you are making box joints. There are many ways to skin a cat and in the end you have a skined cat. But usually the real question is what is the most efficient way to skin a cat. In the case of box joints your skinned cat is the I-Box.
Guy I don't disagree with you but hear me out (short version). Speaking only for myself, if your not careful your spending most all of your "Shop Time" building jigs If you can) or your buying the jig that you didn't want to take the time to build in the first place. Now if you have a lot of "Shop Time" or a lot of money to buy the next shiney jig then more power to you. My shop time is limited as well as my shop money.
In this particular case "dovetail jig" I spent $180 9 years ago for a multi joint nice PC 4212 jig. After a year or 2 I had stopped using it. Now in 2019 I decided to pick it back up for the same reason I bought it... to have the choice of multiple joints to use in making boxes. My question in Posting was about the orientation to end up so the grain would line up. No one had the detailed answer but you took the time and kindly answered the smart rational way for me to find the answer, again thank you.
Just a little bit more. In late 2018 I wanted to replace my shop made table saw sled with a brand name sled and one with an extremely accurate miter. The final 2 choices were Incra or The Dubby and (Right or Wrong) I went with the later mainly because I was using it for Frames it came out cheaper in the long run. Now Incra is jam up and its jigs have the same quality. If I had gone with Incra I would have gone with the best one(5000?) and added the box joint and I think they have a wooden hinge accessory. So with money in mind I went with the $180 Dubby and Did not spend the $329 for the 5000 decided to use my PC 4212 for box joints, through dovetails half blind dovetails and not buy Incra's for $170 but put the wooden hinge thingy on the wish list.
Is Incra the best fastest way to make box joints? Yes you are right. Are there better through dovetail jigs yes especially for the router table absolutely.
For me If I don't watch myself I end up taking way too much time building jigs which many are not often used or buying new jigs one after the other.