I haven't used twilight check in but I know we could use the Downtown Disney check in when we flew with Jetlife. It was a Virgin Atlantic perk - not a Virgin Holidays one
I don't think you can. I flew with Virgin from Gatwick in May this year using a Continental ticket from Expedia. I thought as they are partners on the flight I could use the twilight check in but after contacting Virgin they informed me that I couldn't.
I'm sure you can use the twilight checkin - Jetlife are just the tour operator, and your flight is with Virgin Atlantic - just as if you booked your holiday through Virgin Holidays.
If you are booked on the Virgin coded flight (VS...) then you shouldn't have any problems.