For me it's a matter of principle. In theory, the publisher designs the book exactly the way they want it to look, and that's what I want to see. Now I realize that we're still probably years away from such an ideal world, and that in practice, probably fewer than 20% of eBooks have actually had that much thought put in by the publisher. So, if Kobo is doing this to try to clean up the messes of most publishers, then, "I get it". But I still don't like it. I don't think it's appropriate for the device to ignore/override any detail, no matter how seemingly inconsequential, that is in the original file. Of course it hardly changes the actual reading experience, but it just doesn't sit right with me.
A simple solution (or maybe it's not simple, I don't know what the code looks like) would be to offer a Font preference under Settings that allows a choice between "use book defaults" or "use Kobo's fonts".
And for those of you who do want a more tangible reason why this is a (still small) problem - I recently read Kurt Vonnegut's "Breakfast of Champions". In the book one of the characters is described as having committed suicide by "eating Drāno" (that's the letter 'a' with a macron). On my lovely Kobo, which I love in every other way, the character ate "Dr?no".