It is a mixture of both I guess. To use your example Zaev, Lord Marrowgar: it is impossible for a rogue to continue to damage the boss while out of melee range. By contrast, it's hard for a hunter (especially) to keep damaging Marrowgar while within 5 yards of his hitbox. But there's a part of most fights that requires downtime. Deathwhisper is a good example of a fight where there can be considerable downtime when you add up all the target switching.
It's reducing the gap between the two measures that's important - thereby increasing your raid effectiveness. If we simply used actual DPS to measure performance, I could blow all my CD's at the start of the fight, call my pet back and afk for rest of the fight. But, my DPS for the length of the fight would be really low. So, as I said, it's reducing the gap between the 2 by maximising your dps time that counts.
In the end, damage to boss counts most, but that is a rather blunt way to view perfomance, especially when you have so much more from a raid report. Different fights favour the different classes. It's important to look at the bigger picture and not just damage done. The one big thing you're looking for is lazy dps'ers who can put out ridiculous burst and then back off or worse, stop damage, just to 'massage' the dps meters. It is not a dps race, it is a 'lets get the boss down as fast as we can race' :P