Well, even the doom horrors aren't anywhere close to as powerful as Scion.
When Scion has all shards and is traveling through space to another planet? No. Here? Just maybe weak enough... and doom horrors might not be limited in interdimensional travel, so they could not attack avatar of scion, but his actual body on another parallel Earth.
Parahuman's shards are programmed so that travel to worlds with shards is forbidden and Scion being blind spot to precog and other extrasensory perception. Doom horrors and maybe Taylor... no such limit?
But, yeah. Too much collateral damage with human getting marked by random horror attack. Lets leave marking for "Humanity lost, let him not escape unhurt, he will die with us".
On ethereal quality.... Shadow Stalker gives any clue how to deal with this, she used variant of etherialness? Scion wouldn't attack only by hitting you with his fists, but his golden light that could count as supernatural/magic enough.
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With Taylor's scales being all 0, beside magic 1 one. Brocton bay being all scales at -1, except magic at -3... wouldn't state of city slowly improve in all scales, not just magic, anyway, as she spreads her dominion over whole city?
And rituals that search for Places of power which make gems... when she gets them... how fast could she find those places, as in what area they cover? Street, district, whole city, more?
As aditional sources of gems, once supplies start running dry. Weren't Temples and other holly places also creating astral pearls as there are no holly gems? Astral is also connected to divine as it summons angels and divine national summons.
Of course, normal temples you build don't make pearls. Ones making them are found ancient temples, or special temples found in nation's starting province, which are part of their backstory and can make any gem beside pearls depending on story.
Few mage creatures that could live underwater sent to go explore the sea? Sea has mostly water, but also nature, astral and death gem producing sites for example?