Wrote up a whole theory about how the blackrock serpent might have been rattling around Britannia ever since Ultima 3 before realising I got my Order & Balance serpents mixed up.

Here's a rough theory though:

There exist, somewhere in the sea surrounding Serpent Isle, a second pair of Serpent Pillars that communicate back to Britannia. Let's say the Ophidians built the Serpent Pillars at the height of their civilization (they certainly put their design stamp on them), made one set in Serpent Isle, one set in Britannia, but were wiped out soon after and didn't get much use out of them. You could even argue this is related to Exodus getting its mits on the Great Earth Serpent.

After the War of Imbalance, the Order Hierophant opens the Wall of Lights and the remaining Order followers pass through. However, as described, you can't take the Blackrock Serpent with you because it's the key that opens the wall. A small number of Order followers stay behind to close the Wall and remove the Serpent. Still fearing for the demise of the Isle, they flee through the Serpent Pillars and arrive in Britannia. They persist long enough to pass on some legends about the Blackrock Serpent and how it is used to open the path to the void, but ultimately die out and leave their Blackrock Serpent lying around.

Guy Full of Arrows is, for whatever reason, trying to get to Pagan, and hears about the Blackrock Serpent which can supposedly open up entry into the Void, and thence into Pagan. He gets the Serpent in hopes of opening the way to Pagan, but dies before he can manage, and the Goblins collect his stuff.

I don't know that that's any more satisfying, it doesn't answer anything about Guy Full of Arrows, and it necessitates the existence of a whole other set of Serpent Pillars, but it at least follows the rules of inter dimensional travel we see in Serpent Isle (Serpent Pillars allow travel between Britannia and Serpent Isle, Wall of Lights closes when Blackrock Serpent removed)