When first introduced the concept of the Reaper chest was that it doubloons were a valuable currency and Reaper chests awarding them was supposed to turn these chests into beacons for PvP to battle over this better currency. Doubloons have since lost pretty much all purpose. Reaper Bounties were introduced as a nice chunk of gold. Even they are rarely gone after or fought over as 10k gold really isn't much to be worth the trouble of going out of your way to grab them.
Making them worth allegiance for the new factions would bring back their value as a PvP beacon. It could be something as small as Reaper chests are worth a loss worth or allegiance and a Bounty would be worth 2 losses. Some might argue this would allow FoTD stackers to farm PvE to gain.. True. But stacking FoTD is already setting yourself up to be PvPed anyway. But if its really that much of an issue you could just remove them from the FoTD loot table and put something else in their place.
Or replace the shipwreck reaper chests and replace those with a new reaper chest type that's for allegiance.
