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My first thought was about the centuries-old theatre trick: Harry hides a few drops of red paint in one hand, presses that hand on his forehead because “the scar hurts” … and voila, a bleeding scar.

Your thought seems simpler, though, as well as plausible:

The pain that flashed through Harry's scar was searing, it made him cry out and a red haze appear across his vision

(chapter 114; although I’m not quite sure whether that really refers to blood from his scar, or just garbled sensory input caused by the resonance)

The stage seems to be set for a sequel adventure series, The Three Immortals. Three great heroes, each blessed with a fragment of immortality, work together to fend off the forces of destruction and bring true immortality to all of humanity.

Unicorn Girl, filled with the life-giving, regenerative powers of two noble magical creatures. Her mind captures everything that she sees, with amazing fidelity, while the purity of her heart pulls her to do what's right with similar fidelity. Some call her "mudblood", in honor of the ancient myths about the creation of man from earth, because the power to re-create herself flows continuously through her veins.

Mr. Physics, the culmination of the great Peverall line which has sought immortality for generations, is the heir to many great and powerful magical artifacts. But it is his deep and detailed knowledge of the laws of the universe which grants him his greatest power - the power to make anything out of anything, even reshaping his own body. He has made a solemn vow to protect humanity, with Unicorn Girl as his moral compass.

The mysterious Cloud has dark secrets which are hidden even from himself, but his mind still holds a wealth of ancient lore to share and an intellect so sharp it can cut through any facade or riddle... except perhaps his own past. This great mind is backed up, a hundred times over, in a vast network which allows him to be reborn in full force should his body ever fail him. The first to reach immortality, Cloud helped bring both his companions into their powers.

Voldemort allowed Harry to be a threat because otherwise there wouldn't have been a story.

The problem is that he did so in a way that feels inconsistent with the rest of the story. Most villains in most stories aren't the type that would relieve their nemesis of his limbs, mind, and freedom to move outside a little box. Sauron didn't seal off the Cracks of Doom, or even post a serious guard around them. The Emperor didn't place the shield generator on Endor in a hidden underground compound guarded by a small army. A great succession of villains have failed to just shoot James Bond. HPMOR!Voldemort would do all of those things, because from the start his extraordinarily high intelligence and skill at what he does have been cornerstones of his character. When he makes a mistake, many readers will assume (and have assumed, usually correctly) that it is a deliberate ploy. Mistakes as bad as what we're seeing here aren't just folly; they verge on character derailment.

I believe Voldemort was unconscious at the time, following a magical feedback mishap at the conclusion of his duel with Bahry. Bellatrix was awake, but probably not very coherent after eleven years in Azkaban, and Voldemort strikes me as the type to dismiss confusing reports from unreliable underlings.

Didn't V see at least the results of a Partial Transfiguration in Azkaban (used to cut through the wall)? Doesn't seem like something V would just ignore or forget.

In pouch, no. Transfigured in his glasses, maybe... but Harry is not allowed to move his hands to touch the glasses.

Unless the glasses already a contain a killing machine operated by eye movements. Then Harry can kill everyone with a blink of an eye. (Undiscriminate killing would also hit Hermione, but she would survive.)

In Chapter 61 Dumbledore says:

"[...] But his second avenue is nearly as strong: The flesh of his servant, willingly given; the blood of his foe, forcibly taken; and the bone of his ancestor, unknowingly bequeathed. Voldemort is a perfectionist -" Albus glanced at Severus, who nodded agreement, "- and he would certainly seek the most powerful combination: the flesh of Bellatrix Black, the blood of Harry Potter, and the bone of his father. [...]"

Ch. 108

"What did you do with Bellatrix once she was out?"

"Ssent her to a peaceful place to recover sstrength," Professor Quirrell said. A cold smile. "I had a use remaining for her, or rather a certain portion of her, and on my future plans I shall not answer questions."

Ch. 112

For a second Harry's mind couldn't process what he was seeing, and then he saw that Voldemort was holding a human arm, severed near the shoulder; it seemed too thin, that arm.

The Dark Lord pressed his wand to the flesh above the severed arm's elbow, and the fingers twitched, twitched like they were alive; by dim moonlight Harry saw a darker mark appear on that flesh, just above the elbow.

Is everyone else making this interpretation?

I rather doubt it; he might still be “guarding” that corridor.

On the other hand, Lucius Malfoy should be there. His reaction might be interesting, given his previous, rather unusual encounters with Harry …