The new allele does not magically change those that carry it into new species
Agreed.
There is no suggesting of the sudden formation of two species and one outcompeting the other.
Agreed.
In situations were an entirely different species enters a niche, there can be competition that leads to some sort of equilibrium between the species, failure of the invading species or success of the invader in taking over. This is backed up by real world evidence. Invasive species. You are mixing the two into something erroneous.
Invasive species have nothing to do with speciation.
The theory describes the change and why. It does not predict what a specific mutation will do within a population.
Per the ToE, new species don’t just pop out to from another. The change is gradual. A new allele /variant can only emerge within an existing niche and will continue to be the same species. (The new allele doesn’t preclude interbreeding of the variants.) Even if a variant becomes isolated geographically, it doesn’t change the fact that it’s not a new species, similarly the emergence of another new allele will not change the isolated variant into a new species. It will continue to be the same species unless somehow it loses the ability of interbreeding with original species. But if that happens, it doesn’t mean that original species should go extinct.
The process repeats randomly, multiple species may emerge and all may survive. As long as ecological conditions/resources remain tolerable, a species that continue to be reproductively successful should not go extinct. Variants/new species may expand to new geographical territories but all can very well coexist.
Losing the ability of interbreeding in the speciation process means that future changes in one species may not directly impact the other and all species can coexist independently.
If this is the case, again, what is the reason that all alleged transitional hominid forms went extinct but the chimp survived? This may happen only in the case that intermediates never lost the ability of interbreeding and continued to evolve. But this hypothesis entails that no speciation was ever involved. No speciation ever happened (because speciation is necessarily associated with the loss of interbreeding capability). However you look at it, you will see that these predicted scenarios are false and not consistent with real world observations.
Consider the real world example of Humans in different geographical zones, they may have differences but all continue to be the same species and capable of interbreeding to make fertile offspring. Even humans in the most isolated zones didn’t change into different species.