@capn-mcquacken
The emissary system is risk vs. reward. When you put up that flag, you accept the risk that a Reaper could drop on you at any time. You just want to be an emissary without the risk... if you want to stop being hunted by Reapers, stop asking Rare to step in and change things for you. Just don't raise the emissary flag.
It's said so much on the forums, but it's so true. Only carry on your ship what you're willing to lose. If you have a whole Grade 5 haul that you lost, that's also your fault because you hadn't sold earlier. "But you don't sell until you are Grade 5!" Just another risk of being an emissary. You take a gamble every minute that you aren't selling, and waiting to get to Grade 5 is just greed getting in the way of fear.
If you don't want to get sunk with all of your loot, don't raise an emissary and/or sell often.
Making Reapers only see Grade 5 emissaries would serve to make their G5 ability useless, because most G5 ships only stay that way for long enough to sell. Not much time for a Reaper to do anything.
You seem to be mad for getting sunk by Reapers and then want portal hopping removed so it doesn't happen as often. What are you trying to do? Reduce your risk while keeping the same payout. What are PvE server advocates trying to do? Eliminate risk while keeping the same payout. You're not doing the same thing, but it's the same sentiment and one that shouldn't and hasn't been catered to by the developers.
What portal hopping does for Sea of Thieves is help inject more risk for emissaries. This is a good thing, because if PvP didn't exist at all, the loot and game would be meaningless. So, the more PvP, the more actual value there is for loot, because selling loot means that you probably had to evade or engage in PvP.
Just look at Athena's Fortune level 30. The fastest way to get to 30 is Legend of the Veil voyages, but doing those voyages brings in a higher risk of PvP. Which means that a high level in Athena's Fortune represents a player who must overcome hardships more often.
Injecting more risk for emissaries is also important in a game where there is a 5 ship cap and a player limit. Meaning, in an average server there is less chance for PvP because there are less ships, and also servers are mostly solo sloops because of the player limit. In a game with servers like this, portal hopping is needed to continue to inject danger, and reduce the number of "natural PvE servers."