I wouldn't argue with in-EVE science about it, because it's merely techno-babble. (For example: If you look at convergent evolution in e.g. moles and the mole cricket, then you will see that covergent evolution is about phenotypes, because the phenotype interacts directly with the environment - not the genotype. Mole crickets don't share more DNA with moles due to 'convergent evolution' than any other cricket does. Convergent evolution explains phenotypical similarities despite genetic differences.)
Even thoug the Fedo 'originated' by PF on Palpis and the slaver hounds on Syrikos and are 'native' to these planets, that doesn't mean they are alien species in the sense of not descendants of life on earth. If you can terraform entire planets, you certainly will be able to modify species to fit niches there - there's no reason against assuming that they are engineered species.
That is as well true for methane breathing species like the Hanging Long-limb, especially as they are eadible. It is quite probable that truely alien life forms wouldn't be eadible, for the sheer number of statistically available amino-acids, which would quickly become problematic for earth-life as they'd interfere with all kinds of metabolic processes. Even if they basically used the same amino acids, there'd be a 50/50 chance of them being mainly based on the D_stereoisomeres instead of the L-stereoisomeres, making one in two alien lifeforms by statistics quite deadly (It's like trying to drive on the right side of the street in the UK.)
So, it would be more reasonable to expect the more exotic life forms of new eden to having been engineered by the first terran settlers, rather then to explain them as 'aliens'.
Anyhow, I think CCP doesn't really mind one way or the other and left it vague if for no other reason than the one that they don't care. So, why should we care too much? It's not that we really need it to decide on this. The only data we have on how living beings work to approximate from are beings on earth any way.