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.
As a simple matter of fact, Voldemort is stronger than Harry in basically every way, other than Harry's (incomplete) training in rationality. If Voldemort were a good enough planner, there's no way he could lose; he is smarter, more powerful, and has more ancient lore than any other wizard. If Voldemort were also rational, and didn't fall prey to overconfidence bias / planning fallacy...
Well, you can be as rational as you like, but if you are human and your opponent is a superintelligent god with a horde of bloodthirsty nanobots, the invincible Elder Ligh...
This is a new thread to discuss Eliezer Yudkowsky’s Harry Potter and the Methods of Rationality and anything related to it. This thread is intended for discussing chapter 114, and also, as a special case due to the exceptionally close posting times, chapter 115.
There is a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author’s Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)