: Not entirely surprising, given that 343 did not pursue the H=F avenue that
: Contact Harvest did, but it's interesting that the Luminaries as described
: here do not function as the Luminaries in Contact Harvest did—that is,
: detecting humans, but rather activated Forerunner tech.

Why is that not a filter option?
"Luminary, display all data."
"Luminary, filter out all Human symbols."
"Luminary, filter out all geological curiosities."
"Luminary, filter out all traces of Human ancilla."
"Luminary, save the report and transmit a copy to High Charity."

: To me it was
: always odd that the Luminaries would work that way—leaving aside the
: dramatic reveal that humans are Forerunner inheritors, how did the
: Covenant not easily find and exterminate every human hole via that method?

Why wouldn't they?

This is supposed to be a war of extermination. The Covenant are supposed to be a force that can't be fought, only delayed. Having Human survivors crop up in every arcology and glassed colony rather undermines that point.

If I had to reconcile the survivors seen in The Cole Protocol, Glasslands, and Escalation with the ubiquity of the Covenant Luminaries, I'd go with a combination of factors:

-Luminaries are as expensive for the Covenant to manufacture as MJOLNIR is for the UNSC to manufacture. Therefore, during the war, they were typically installed on flagships or handed out one per flotilla. If the ship that carries a Luminary is destroyed, the Covenant cannot spot well-hidden bunkers and stealthed habitats. The system is then scheduled for a later sweep, which was not always carried out.
-Manufacturing defects in the Luminaries allow small groups to go undetected in certain circumstances. The circumstances change from Luminary to Luminary, which is why the Covenant usually assign at least two per fleet.
-Luminaries have a short operational life, measured in tens of hours of operational life before the sensors burn out. To extend this life, savvy users operate them on an extended duty cycle, with only a few minutes of active scanning every hour. This is how Prowlers usually get the jump on Covenant warships.
-Humans who are near death or in a medically induced coma are registered as "dead" by Luminaries, which is why Mike Baird wasn't killed in his sleep in Midnight in the Heart of the Midlothian. There are plenty of stories about people who recovered from death's doorstep after a glassing, only to die slowly and painfully months later as their survival equipment wore out and what little food they could scrounge was consumed.
-After the early stages of the war, bands of refugees journeyed through the front lines and set up hidden colonies in exterminated systems. These refugees were hostile to or persecuted by the UNSC, and were willing to gamble that the Covenant wouldn't sweep through a given system a second time through.