Because "completely" isn't read to include everything down to tardigrades and E.coli.
To start, here are examples of (seemingly knowledgeable) people using that phrase:
"The Atlantic lowland forest of Brazil comprises a completely separate biome from the Amazonian forests to the north and west, and is home to a rich array of endemic fauna and flora. Among over 200 endemic birds are at least ten endemic genera, including such spectacular species as the Seven-coloured Tanager (Tangara fastuosa)" - https://archive.org/details/atlasofbirdsdive0000unwi/mode/2u...
"Now called the pine-hemlock hardwood forest, or northern hardwoods, it had survived the axe, fire, and insects, and lay as an ecotone between deciduous forest to the south and coniferous forest to the north. Shelford considered it to be a third association of the transcontinental coniferous forest biome, while Clements viewed it as a completely separate biome." - https://archive.org/details/pioneerecologist00crok/mode/2up?...
It start "Plant ecologists have regarded an essentially complete difference in climax dominants as the basis for the recognition of the major plant communities called plant formations." then mentions how that "usually includes some wide-ranging species among the dominants" ending "It is the purpose of this paper to show that it is not always feasible to make sole use of the criteria of plant dominants and maintain the integrity of some of the impor-". (For a summary of the paper, go back to https://archive.org/details/pioneerecologist00crok/mode/2up?... .)
So "completely separate" should be read to mean something more like "essentially complete difference", and not "absolute difference".
To start, here are examples of (seemingly knowledgeable) people using that phrase:
"The Atlantic lowland forest of Brazil comprises a completely separate biome from the Amazonian forests to the north and west, and is home to a rich array of endemic fauna and flora. Among over 200 endemic birds are at least ten endemic genera, including such spectacular species as the Seven-coloured Tanager (Tangara fastuosa)" - https://archive.org/details/atlasofbirdsdive0000unwi/mode/2u...
"Now called the pine-hemlock hardwood forest, or northern hardwoods, it had survived the axe, fire, and insects, and lay as an ecotone between deciduous forest to the south and coniferous forest to the north. Shelford considered it to be a third association of the transcontinental coniferous forest biome, while Clements viewed it as a completely separate biome." - https://archive.org/details/pioneerecologist00crok/mode/2up?...
We can see the first page of that latter paper at https://www.jstor.org/stable/1930076 .
It start "Plant ecologists have regarded an essentially complete difference in climax dominants as the basis for the recognition of the major plant communities called plant formations." then mentions how that "usually includes some wide-ranging species among the dominants" ending "It is the purpose of this paper to show that it is not always feasible to make sole use of the criteria of plant dominants and maintain the integrity of some of the impor-". (For a summary of the paper, go back to https://archive.org/details/pioneerecologist00crok/mode/2up?... .)
So "completely separate" should be read to mean something more like "essentially complete difference", and not "absolute difference".