Conventional wisdom seems to be, as you note, that in doubles it is best for the first (usually lower) barrel to shoot high for the first shot (a rising target) and the second (upper) barrel to shoot a bit flatter, since the second target is normally slowing down by the time you get to it. Many over/under barrels are regulated this way (My Beretta 682 o/u barrels shoot this way, for instance). While this difference in POI between lower and upper barrel is, of course, set/regulated at the factory when the barrels are put together, the actual POI will, of course, still be set by the shooter, or adjusted through use of the adjustable comb, or rib (which is now sometimes being used on o/u barrels). That is, you could set your comb so that your POI using lower barrel is, say, 80/20, and the lower barrel might then have a POI of something like 60/40 (or whatever difference in POI the factory set them for), perhaps only 70/30 for the lower barrel and then the upper would be(in this scenario) 50/50. A few guns (such as K guns, and the Remington 3200) have replaceable/changeable barrel hangers, which allow a user to change the lower and upper barrel relationship a bit, so these guns could have a user change in upper and lower barrel POI.
Jim R