I'm trying to catch the gist of the sentence - not this particular sentence I mean, but assuming the sentence you're working on has the same structure!
Are you saying (the equivalent of):
It's not just that, trivially, it relates to some penguins - importantly, it relates to some emperor penguins
It's not just that it relates to some penguins - it relates to all emperor penguins
It's not just that it relates to some penguins - it relates to all and only emperor penguins
... or what?
Sorry if I'm overcomplicating this, but the sentence seems a bit weird as it stands because obviously something that relates to all penguins is going to relate to emperor penguins (cf. "It became evident that it not only related to fruit but to apples")... so I figure you must be trying to say something about "it's not penguins in general, it's emperor penguins in particular", but I'm not sure what? In any case, I wonder if tweaking the wording might remove the need for emphasis.