In general people have come to expect that hitting return once in a comment field on GitHub will produce a newline, having been the case for many years, so we try to preserve that expectation. Hence not changing the option being used when rendering comments.

Conversely, they don't expect the same from Markdown files stored in their repository (e.g. I put each sentence in a paragraph on its own line for my blog, for easier diffing and editing). Additionally, we couldn't normalise these documents even if we wanted (to prevent everything breaking by being over-vertically spaced). Hence not changing the option being not used in this case!

Because using the new display format with a non-normalized source would break the display.