So if a new first turn was implemented where both teams get to reposition their armies without crossing any borders or firing at all, it would reduce the chance that phantom league could gain an advantage in the first turn. The phantom league could then go first as usual.
My take on this idea: It has a lot of merit, and probably should be considered (sounds like Vic and team have already come up with a descent solution), but there are two problems with the listed approach:
1) It slows the game down
2) It really doesn't give you very much benefit to the FNU
3) It might actually give more advantage to the PL
The second and third ones needs a little explanation: Basically, when you disclose your initial allies as FNU, you have to chose where to put them. And unless you choose entirely mobile forces (tanks, transports, bots), you will have a difficult time adjusting your line to the enemy's disclosure if you haven't put your initial forces in the right place. The problem with always choosing mobile forces, too, is that they are very expensive, and not cost effective if you don't have a running battle.
For the PL, they actually might have more advantage, because regardless of how the forces are redistributed, the PL gets to strike first, so if they have a chance to readjust their units they may be able to plan out a worse first strike then previously, or even change from attacking a neutral country they originally chose to a disclosed ally of yours.
As far as the discussion on advantages, I agree with Mrakobes. It is only in certain situations that it gives a huge advantage, that being when the PL happens to disclose next to a FNU disclosure. These situations are possibly more common on smaller maps, but they happen very rarely on the larger maps. You're likely to be more affected by SA positioning than who plays what (hence our discussion in this forum on SA positioning strategies).