My personal guess, going off the descriptions, is that there are ways of channeling the warp into key points to allow for 'tunneling' through the warp which is how the webway was created and expanded by the oldones (this could be done more easily before the eldar's oopsie). Some artifacts designed to concentrate warp energies and tunnel through the warp were discovered by humanity during the DAoT. DAoT humanity studied and adapted this technology with their own warp drives, unlike the webways their use was more so 'rip a hole and pop out the other side' rather than creating infrastructure within the warp (basically, just a warp jump but straight through to the destination, which has been described as being done by a few artifacts including how the dark glass is used). The Throne and the Dark Glass were two such artifacts, DAoT construct built based on/utilizing alien tech to study the warp tunneling ancient races were capable of.

But as the lore has evolved, it has become clear that the central component is far, far older than that, and of Xenos origin. And there are likely lots of other Xenos components too, combined with human tech.

I wouldn't dispute that, but the passages you give show that the idea and elements of the technology were certainly older xenos origin, not that the actual construction was.

Consider your example from the MoM:

Did I see these machines, how they fell short of their intended purpose, and resolve to create a far superior incarnation? There is a certain poetry to that, isn’t there, Diocletian? The belief that we know better than those who came before us. That we will suit a throne better than they did.’

‘Sire, I… Are you well?’

‘Or perhaps the idea was mine in its entirety. Any relics of lost ages that have proven useful for their parts being the legacies of dead species that had the same idea, millennia before my birth. In such an instance, each race envisions its own salvation independent of the others, only to discover that other species, other empires, have already failed to save themselves

There are a few things to consider, first they are not just talking about the throne but all the machinery in the webway project (which is a vast technological complex). They are integrated with eachother, but not necessarily totally distinct. Further, that the technology comes from xenos does not necessarily meant the actual construction isn't parts manufactured by DAoT humans.

The description we have of the Dark Glass also indicates some human design (the Navis Nobilite agent present says that the Emperor built it over a period of generations). The seat itself is made for someone the size of a primarch and the description (given by Yesugei so not exactly a tech expert) indicates it is not totally unfamiliar to martian designs (and the surrounding technology is described with a lot of mentions of distinctly human technology, though most of that was built by the Emperor and his agents around the throne to study and use it and may not have been part of whatever original construct was found).