The money isn't the main incentive to lower flag anyway, its more about sticking it to ships that chase you all over the map.
Instead, I think there needs to be opt in, "competitive" voyages while flying emissary flags that award extra money / special loot used to unlock cosmetics. The challenge is making these voyages not farmable by alliance servers.
These opt in voyages could be posted by Reaper's ships looking for a challenge, and would be a way for the reaper's ship to ensure they are pvping against ships willing to accept the PVP challenge for the chance at more reward.
Example)
Reapers ship posts an opt in voyage which appears as a reaper's voyage available at every outpost. Only one ship is allowed to accept the actual voyage while flying an emissary flag, but any number of reaper's ships can also pay to be part of the hunt. It could cost something like 50,000 gold to post but would be refunded if nobody accepts.
One such type could be a reaper's gold hoarder vault.
A gold hoarder emissary votes to accept the voyage, and pays 50,000 gold as well. This is the buy-in, and cements the voyage as a zero-sum game (a winner and loser) so there can't be any farming in alliances. Players could still use this to "transfer" gold I guess, but maybe it could be what Reaper's get as their grade 5 reward so it is on a pseudo-timer (the ability to post one Reaper's voyage per grade 5 earned).
The gold hoarder ship gets the same compass and everything as before, but reaper's ship also gets a compass which points in the general direction of the accepting ship (can't see ship on map as in current system).
The twist may be that the reaper's ship needs to engage the gold hoarder ship before the vault is opened (hit them with a cannonball). If they do not, the loot from the vault is not worth any additional multiplier to them, and they lose their 50k investment.
If they do manage to locate the ship in time and sink them. The voyage progress gets turned over to them instead, they get their 50k back, and can still earn the extra value from the vault.
However, the accepting gold hoarder ship can still track them down if they do sink and get the vault loot if they knew which island they needed to go to. They would effectively switch places.
Just my thoughts, needs some more development, but it'll never happen because c'mon, Rare doesn't look at the forums XD