Other than receiving slightly better voyages the higher your reputation is, there isn't really a benefit to having the individual factions reach level 50 except for when you get all three of them and you become a Pirate Legend. I am suggesting a couple additions that would make use of the individual mastery.
Master Gold Hoarder: Encrypted Maps - Special maps that only a master gold hoarder can view and reveal its secrets. In the end, these aren't protected by lowely skeletons, but an entire crew and possibly their captain!
As a master of the gold hoarders, you have dug up treasure from every corner of the Sea of Thieves. Thoughout your travels you have stumbled upon ruined villages, ancient tombs and had mystic encounters, all of which has increased your knowledge of ancient texts and hyrogliphs. These experiences and ultimately the knowledge earned allows you to decypher maps that cannot be read by those who have not reached rank Master Gold Hoarder.
Master of the Order: Talking Skulls - Instead of glowing green, a skull that glows yellow (or another color) can be encountered and only a master of the order can listen to its whispers and decypher its secrets. These secrets would yield a map of the island where the skull was found!
As a master of the order, you have given your body and soul to the order by battling legions of skeletons. Since the beginning of your mystic journey, you have heard soft sounds eminating from the skulls of the vanquished captains. However, as time passed and your experience in the arts grew, those soft sounds turn into whispers. These whispers often divulge the location of buried treasure but go unnoticed by those who have not reached the title of Master of the Order.
Master Merchant: Smooth Talker - You are able to get an extra percentage (coin, not rep) for items turned in (any faction) due to your connections within the Merchant Alliance.
As a master merchant, you have bartered with everyone from The Ancient Isles, Wilds, and through to the Shores of Plenty. Working your way up from a lowely chicken chaser to a pervayor of fine goods, your reputation preceeds you wherever you go. The knowledge of the seas and the fauna of the lands fetches you a higher percentage than those who have yet to achieve the position of Master Merchant.
These are fairly rough, but I think the point comes across. The different benefits spread to the other factions and require level 50 for that specific faction, but are not only obtainable by a Master per se except for the Master Merchant.
Master Gold Hoarder: A level 50 Gold Hoarder may recieve these encrypted maps from a standard voyage pickup, but anyone below may stumble upon then via books or bottles and would require a Master to look at the map to decypher it.
Master of the Order: A skull glowing yellow and can found randomly by anyone, or from a slain skeleton as normal and turned in without a second thought. However, a Master of the Order can pull the secrets out of the skull before turning it in.
Of course I don't think these should chain together either. You cannot use an encrypted map to get a chest which may have a captain spawn, then get a skull which glows yellow and provides a map when a Master of the Order pulls the secrets from it.
Thoughts?
EDIT: Adding additional suggestions here to keep them near the top.
Adding this to the Master of the Order could be used for Skeleton Ships. You take out a Skeleton Leader (Non-Captain) and their skull whispers the location of another member of its crew. After a few island hops and extracting the information from the skeleton crews, you are given the location of their ship which would have their captain and remaining crew. But this may limit it to having a Master of the Order on your crew...
Perhaps have these perks start at level 40 and scale up as you get to level 50.
