Glad you got ack. from Kobo Christopher. There were some questions about what exactly the effect of all this is. The explanation I've given so far is a little technical, and with the smokestcreen from the chearleading section, it can be hard to communicate the implications without sounding like a raving lunatic. (insert if it quacks like a duck comment here.)
So here is a screenshot of the same book. Decide for yourself if the changes are annoying or inconsequential.
http://www.mediafire.com/i/?1x85e61lb26j6bl
The one on the left is purchaesd from Barnes and Noble. The one on the right is purchased from Kobo. Here you can see the changes that are wrought by the insertion of Kobo.css and kobo code throughout the text. (I call it Kobo code becaue it's conveniently labeled kobo, so I assume Kobo is the one doing it. We all know what can happen with assumptions, however.)
The changes that I have found are:
Larger text (the least bothersome, since all readers allow text size adjustment).
Doube spaced text.
Space between parapgraphs, which can make it more difficult to decipher when an actual scene break occurs, since several books use a space between paragraphs for those.
No paragraph indentation.
Complete removal of margin. This is more bothersome on actual reading devices, since the text will be flush against the bezel.
And the most recent observation, look at the second to last line on the Kobo version. Notice that only and one have no space between them. This has happened to all italized text in both books I've sampled. If there is italized text within a paragraph, space after italized text gets removed.
As for how many books are affected, 2 out of 2 new books I purchased from Kobo got this treatment. (Thirteen orphans and Saint's Astray.). Supposedly, not all books are affected. However, 2 out of 2 is enough for me to avoid buying any new books from Kobo until this issue gets acknowledged and addressed.
Of course, if none of this bothers you, then carry on and ignore the ranting lunatic.