That's a huge stretch. Even if some alien engineers did take H. heidelbergensis and manipulate its genes to produce all the humanoid races, it seems unlikely that they'd all just coincidentally happen to end up being given the same final body plan, mouth shape, vocal tract structure, etc. that H. sapiens evolved by natural means.
Granted.
Your proposal would make more sense if it had happened within the past 40,000 years, and that wouldn't explain more ancient species like the Arretians, the Tkon, and the Sky Spirits.
That's true and the really ancient species are the biggest problem with the theory. Though, I don't think the seeding needed to be one event. There could have been multiple extractions over time.
I like hard science fiction too, but an important principle of science is the principle of elegance -- the more convoluted a hypothesis is, the more arbitrary ad hoc assumptions you need to pile onto it to force the desired answer, the less credible it becomes. Personally I would prefer it if a universe of humanoids were explained through the seeding of human populations, but that just doesn't fit the available evidence, and the last thing any scientifically minded person should EVER do is place one's preferences above the evidence.
That's true. And in reality, it's never aliens, until it's aliens. But operating from the standpoint of a universe in which sentient, non-malevolent, spacefaring aliens exist. Having a seeding event is not an unreasonable conclusion. So lets presume that a seeding event(s) is the cause of all "aliens" with a modern human human body type. That is a reasonable assumption. The problem is aliens with a modern human body type that predate modern humans.
These are presumably (in no particular order) the Tkon, Sky Spirits, Sargon's Species, the "The Chase" aliens, the Bajorans, the Organians, and possibly the Cheronians (Bele and Loki).
I think the easiest ones to dismiss would be
Sargon's species as we never actually see them nor is it confirmed that they are ancestors of Vulcanians.
SPOCK: That would tend, however, to explain certain elements of Vulcan prehistory.
That's about all the confirmation we get. Perhaps there is something more complex going on, but there is little evidence that they actually are ancestors to the Vulcanians.
Next would be the
Organians. They evolved into energy beings millions of years ago. So the big question is did they look like modern humans BEFORE that evolution. We know that they were "humanoid." To what extent did they look like humans? Two arms two legs and a head. While rare, it is not out of the realm of possibility that they had a general body plan similar to ours. Perhaps the reason they appear as modern humans is because they took that form when humans are involved.
The are interesting because there were hundreds of millions of the people right before Bele started perusing Lokai for 50 thousand earth years. So unless we're willing to do a little rearranging with human evolution then we can put these guys in with the unexplained category.
That leaves us we might be able to explain away the
Bajorans IF we allow for them to have evolved over their long history. Maybe the ancient Bajorans were different, but came to look how they do now as part of the genetic tampering. This one is pushing it a bit, but could be.
That leaves us with the
Cheronians,
Tkon,
Sky Spirits, and
the "The Chase" aliens. So what hypothesis do we have that could explain these?
You can find the concept as compelling as you want, but it is a misogynistic concept with no place in a work of fiction that supposedly advocates for equality and freedom.
I just said it was more compelling than the green skinned belly dancer concept. Several years ago while I was reading the Star Wars Republic Commando series, the author Karen Traviss, included the Star Wars universe's first gay couple. When she was asked why she did that, this was part of her response:
Because whatever your personal prejudices, we live in a diverse world, and people you don't happen to like because of colour or orientation or age or gender are not going to vanish because you don't accept them. I don't like slave-owners and people who think decapitating another being is casual work, but I still write about them, because they're there in the SW universe.
The Star Trek universe is a diverse place. There's going to be misogyny there's going to be hatred, there's going to be racism. In a diverse fictional universe there are going to be things you don't like. Because how the characters deal with conflict is what makes stories interesting. If everything in the Star Trek universe reflected our modern notions of what is good then it would be bland an uninteresting.
Thanks to them there's us. 
I should have said "southern" Africa, not to confuse it with South Africa. They said 70,000 years ago, not 1982. I only saw District 9 once when it first came out, but all I remember is that I sort of liked it and that it had bug-like aliens in an internment camp or something and a human was morphing into one on them.
