Cheaper airfare and delayed final payment aren't fairly significant benefits?
That being said, we, like many others, prefer to have more control over our flight bookings, for a number of reasons. We haven't booked airfare through a cruise line in 30+ years. So if ou can get the same or similar price on your own, take it.
I haven't seen "numerous" comments about lost bookings. A couple, maybe. Things can, and do go wrong with booking direct as well.