It's worth noting that distinct lineages only really happen where there is reproductive isolation and that especially in the modern world no one has a "pure" lineage. Instead you have genetic composition that might have a larger influence from one ancestral population over an other.
There's plenty of reproductive isolation; especially when we're talking about timelines on the orders of thousands of years here. It's a myth that humans are some sort of 'melting pot', as we really haven't been until this latest generation; due to ease of access to travel, better living conditions, access to birth control, and evolving social acceptance.
Doesn't matter if not everyone is traveling far to reproduce, it only takes a few people to introduce a blob of diversity into an otherwise isolated population and suddenly all their ancestors become contributors to that areas gene pool. Without repeated introductions it won't form a large part but it will form part. For example most people have direct neanderthal and denisovian ancestors and it's not estimated that pairing between modern humans and those populations were all that regular an event and yet their genes are everywhere.
It only takes a few people to introduce a blob of diversity into an otherwise isolated population and suddenly all their ancestors become contributors to that areas gene pool.
I researched into this, and was incredibly surprised. The only compatible offspring of neanderthals and modern day humans, were with a male homo neanderthalensis, and a female homo sapien. Estimates are you'd only need 1 successful interbreeding every 70 generations or so.
If it's that low, that makes me ponder: How is it we had both enough genetic isolation for speciation to occur, but enough proximity for pairing with modern humans? Denisovans also interspersed among our population, much the same way.
And if it takes that little, why do we see so many distinct genetic populations today? We see distinct differences in bone structure, birth canal shape, height, metabolism, and the article says even specific notable changes to immune system.
It's because there aren't distinct populations like you perhaps imagine them being, it's more like a smeared colour pallet where one area might be a bit more red or a bit more blue but it's hard to say a specific area is pure blue. The distinct features or populations exist as statistical probabilities based on likely ancestry for a given area. Any given individual in a population probably doesn't express all the "unique" features, but over the total population those features are most prevalent.
Regarding Neanderthals and denisovian populations, they were probably more like what we'd call subspecies in other animals than truly distinct species from modern humans, isolated long enough to build up some unique genetic markers but not quite long enough to be fully separate.
So even in that case, it still makes sense to distinctly identify these groups - even if there aren't hard lines drawn in the sand, it still helps identify bits of the 'tree' of human evolution. We identify dog breeds, and each of those have specific traits that we use to determine fitness for certain tasks all while not being any kind of subspecies of the whole.
Not really, because it doesn't guarantee any specific individual in that population has any of the populations likely traits, it's only useful in aggregate for things like prioritising screening for certain genetic conditions for people of particular back ground. It's useless to determine if someone will be an excellent sprinter or a fighter pilot because ultimately you still have to test every individual anyhow and it doesn't really tell you anything about the "tree" of human evolution which is really a bunch of thick branches all tightly fused together into an indistinguishable single branch.