Another thing you can try installing is the Job Spy plugin. It has an option to convert comments into plain text.
P.S. Please note you'll need to run Polish books, Embed metadata, Convert or use the Send to device function to actually update the embedded comments metadata in the ePub file sent to the Kobo.
P.P.S. I think the latest version of Calibre gets rid of the line breaks when downloading comments metadata. For existing comments though, you could do a search and replace to convert them to space.
Code:
Search field: comments
Search for: \n
Replace with: (space)
P.P.P.S. And for removing <font> tags.
Code:
Search field: comments
Search for: <font[^>]*>(.*)</font>
Replace with: \1