Tracking would be ideal, but if it is too difficult to implement, then an alternative would be a single reward when reaching a second "completion", very high area (e.g. the max 16000 of material mining). With some of the objectives that would be quite challenging even for veteran players. That said, I'm not sure materials (or rubies) would be incentive enough, perhaps some additional runes, rune chests, or challenge tokens?
There could also be intermediate rewards that can be won every time provided they are small (e.g. idols, given that, as it is, the gain of idols in objectives and even in freeplay is insiginificant compared to dungeons)
Incentives for going deep has been a consistent request over the years. I'll add your ideas to the item on the suggestion list and we'll see what happens.