It would depend how much of the spring was exposed above the oil level. If the spring is fully immersed, this is moot.
I guess that would depend on the size of the spacers in the forks. For the 1100, the conventional fork spring has a 130mm spacer between the spring and the fork cap, and the cartridge fork has a 50mm spacer that is retained by a clip that sits just below the fork cap. Given the length of the forks, and the amount of oil inside, when at rest there's no way either of them could ever be fully immersed in oil. I think the spacers in the 1300 forks are longer than the 1100, so it may be a bit different, IDK.
Back to the topic of displacement, let's take a slightly different approach, and add some numbers to help sort it out. Let's say you have a fork inner cylinder with a volume of 500cc, that is empty. You then put the spring in, which has a volume of 100cc, now there's only 400cc of air left in the cylinder because the spring displaced 100cc. Now pour 200cc of oil in, and the air volume is now 200cc because the oil displaced another 200cc. The math will be the same regardless of which way you put the spring in, there will be 200cc of oil and 200cc of air.
Now, one other thing that occurred to me while thinking about this is the fork response to compression. Let's use the example above, and add that the fork slider has 150mm of potential travel.
Let's also state that with the spring oriented with the tightly wound coils down, the oil column is 200mm long and the air column is 200mm long. I suspect the spring in the air might complicate the equation, but let's say by using pv=nrT that if we compress the slider by 100mm, the air pressure in the tube doubles because the air column went from 200mm to 100mm. Now reverse the spring so it displaces less oil and let's say now the oil column is 180mm and the air column is 220mm. I'm not 100% sure, but I think in this spring orientation it would take 110mm of slider travel to double the air pressure inside the tube. In both cases you'd have 200cc of air volume, but its distributed over a different length of tube.
So it seems to me that it might be possible that the fork response to compression does change based on spring orientation, the question is by how much and does it make any difference to the average sport-touring rider on a 700lb bike. This might explain why Honda specifies to put the tight coils down, but I'm just guessing. Curious what others may think about this aspect of the question.