First of all, you don't need to double post like that (and in fact, I believe it is frowned upon.) You can quote multiple people in the same response as long as their posts were recent by scrolling down to the bottom of the reply page and clicking quote from the recent posts there.
Secondly, you can do whatever you want with your headcanon, but the bestiary is first and foremost a tool for the site for people to know what creatures can be collected, what description they have, and what order they were released in. Treating it as if it exists as-is in-universe, with all the entries in that exact order, and anything not listed in it is an undiscovered creature (magical or not) is a choice you can make, but seems oddly limiting. Also if we want to really get into the weeds, many entries do at least heavily imply the existence of non-magical creatures in the world, especially if you take into account both the description that says eating magical companions is frowned upon, and other descriptions implying that magi do eat meat.
But hey, if you want to believe most whales don't exist or are undiscovered in this universe regardless, that's certainly your prerogative, and again, nothing's stopping you from taking that idea and running with it yourself. There's also nothing stopping other people from having no issue with believing they exist and are discovered.
The thread is on the second page of community discussion and you can find it here:
https://magistream.com/viewtopic.php?t=233515