The reason for the game's relatively short length? So that you can finish your journey from beginning to end without any breaks, and with the same companion all the way, should you meet one.
Why there are exactly six spirits of the Ancients who appear to you in the end? They are the spirits who've shown you the visions at the meditation stones in the Beginning, the Bridge, the Desert, the Descent, the Tunnels, and the Temple. That's right, you were seeing a different Ancient every time (they do look the same, but so do you and your Companion), and in the end, they simply all gathered together.
Why do the "War Machines" have no weaponry? They only "eat" the red cloth creatures and store them inside their bodies. The Ancients weren't using them to fight—they use them to steal resources from each other for survival. The machines aren't trying to kill you, they're trying to collect you (or rather, your clothes, especially the scarf) for their absent masters.
Extra Credits brought up an example when comparing the game to the archetypical Hero's Journey, involving the wind serving as Invisible Walls at the start of the game; That it actually serves as as a subtle version of the Refusal of the Call, pushing the player back on the path when they inevitably try to wander off and explore instead of answering the call.
Why does collecting all of the glyphs in the game unlock the ability to be a White Cloak? Because you were focused on doing the exact same thing they did, collecting as much energy as you could find with little thought for any consequences your actions may have caused. And why does being a White Cloak let you regenerate energy without singing to anyone? It is implies that all of the glyphs are the spirits of dead cloaked beings which means that the regeneration ability is caused by their spirits singing to you, just like how the spirits of the Six Ancient White Cloaks sing to you to give you the energy to ascend at the end.
Those crates that contain the little scarves? Those are segments of the War Machines.
In the second-to-last level, the glowing symbols are implied to be the souls of sacrificed robed beings.
All of the markers are implied to be the tombstones. You walk past dozens in the first section. In the second-to-last level, you travel across a snowy hill with hundreds of tombstones, and soon after you and your partner collapse in the snow. During the ending, another tombstone one is created, implying that each tombstone on the hill was from a robed being that didn't make it.
Why are there only two areas that have large groups of tombstones? Well according to the complete tapestry the first group you encountered in the desert belong to the White Cloaks that died in the war, since it shows them buried underneath the markers before leading up to your character's "birth", while the ending implies the second set in the frozen mountains belong to the Red Cloaks that die trying to ascend by reaching the split peak, just like what happened to you.
The War Machines/Guardians faces are masked when inactive. (or right after they turn red when they catch you) If you take a closer look, you can see that aside from a few added details, they resemble yourcharacter'sface. This was done not only to symbolize the Guardians with the darker parts of the past, but also the darker parts of the player'sownself.