So he didn't just imply. He outright stated that Valakians need to be out of the picture for Menk to evolve. Which is quite frankly ludicrous.
No, he presented the other side of the argument in order to point out that there were issues that needed to be considered on both sides. Acknowledging that a side of an argument exists
is not the same thing as favoring that side. Any intelligent, honest person should be willing to consider every side of an issue fairly and openly before making a decision. Phlox was telling Archer that there was a side of the argument that Archer hadn't considered, a side that needed to be weighed against the other.
And is it really ludicrous? Two species competing for the same ecological niche in the same environment are rarely able to share it. Usually one does outcompete the other to extinction. As Phlox pointed out, humans used to share the planet with a number of closely related hominins, but all of them died out except for us.
And one more time: whether it's ludicrous compared to reality is totally beside the point in evaluating a work of fiction. Humanoid aliens are ludicrous. Mind melds are ludicrous. Warp drive and tractor beams are ludicrous. In other franchises, superpowers and wizarding schools and lightsabers are ludicrous. But we willingly suspend disbelief about them for the sake of the story. All that matters should be whether it's the way things work within the fictional universe, and whether the characters' choices and actions make sense within the context of that universe's ground rules.