I just noticed that DOING_CRON isn't defined when running jobs, this could cause unexpected behaviour for some jobs.
While running through WP-CLI, it won't be possible to define it before bootstrap occurs (AFAIK), but defining it late might be better than not at all.
We should do this as soon as possible, but I think that's likely to be when the command's callback fires. We can't really hook in any earlier.
Perhaps an option would be to enhance WP-CLI to accept certain constants on the command line? ie. wp --debug=true --cron=on
wp --debug=true --cron=on
wp-cli itself only sets the constant late, so I'm fine with also setting it late.