I’ve been baking biscotti and the Jewish version, mandel bread, for many years and I know exactly what you mean. I’ve often done the second bake bottom down, i.e., standing rather than on its side.
I’ve thought a lot (!) about why that’s not the general rule, and I can come up with a few reasons. The purpose of the second bake is mainly to dry out the slice. But I can think of many biscotti I’ve had where the slice also turned golden on the sides, and I think that happens when it’s cut side down. In fact, I have the recipe of a long-deceased aunt who actually took it a step further and put her mandel bread under the broiler (to be watched carefully, I’m sure)! I haven’t tried that yet…
Another thing is, if thinner slices are preferred, it’s hard to stand them up and expect them to stay standing when going in and out of the oven. One thing I’ve done is to put a rack across the rimmed baking pan I use and lay the slices on the side. That way they get the heat from both sides. That’s if I don’t care about the golden thing.
I suppose another reason could be if the first bake gets brown on the bottom, standing up might get them too brown, although I wouldn’t have a problem with that because I like them well done.
Anyway, glad to hear there’s someone else out there who thinks about these things!