I know what you're talking about. It seems odd to me that the Bearpaw, which is supposed to be built to be better than anything out there, doesn't have a micro adjustment to allow you to rotate the fletch position slightly to get exactly the allignment you want. The Martin fletching jig is adjustible to allow you to do that. The Bitzenberger isn't adjustible, so you're lucky the stock positions work for you. However, the Bitz indexer has three possible positions you can choose from, and some of their indexers include a blank row so you can drill your own index marks if you don't like any of theirs.
I bought one Bearpaw to try out, thinking that if I liked it, I would buy another one, but had the same problem you did, only for left-wing feathers, where the cock feather ended up a little lower than I liked for my Rick Welch nose anchor (I'm picky about my fletch orientation). I took the thing apart, and decided that short of major surgery, the only fix was to dab a paint spot where I wanted the indexer to stop, which would be just past the divoted index mark. This works, but is not an optimal solution, as I have to remember to move the indexer past the divot to the paint mark each time I use it, and I'm sure I don't line up exactly all the time.
Fortunately, I've started shooting left-handed, and have found that the initial orientation works perfectly for me when fletching arrows to shoot left-handed (a cock feather that was slightly down shooting right-handed is slightly up shooting left-handed), so I will use this as my left-handed fletcher. Whether I will ever shoot left-handed enough to justify buying a second one remains to be seen.
The other thing I don't like about the Bear Paw is that the plastic piece that links the feather clamps to the magnet comes right up to the edge of the feather clamps, so it is easy for any excess glue to spread over it.
At least now you know there is someone who is as anal as you are about these things.