Furthermore, I would suspect they have a different setup for the Mac Pro altogether. ...
As to component lifespan, not really much to worry about. ...
In the case of the OP case at hand, the cooling solutions on AIB cards going into that slot are way better ....
Either way, clocks will drop if the fans can't keep the GPU from exceeding a certain temperature. But yes, we don't know how the Mac Pro behaves with regards to throttling. Nvidia does list the maximum GPU temperature for many of their GPUs (92 C for my 980 Ti, for example), but I haven't been able to find similar info for AMD cards. Can you provide a link to where you got the "around 100 C" or "110-120 C" figures? I've been searching for a while and came up dry.
The contact on the cooler issue is an example of what I'd be concerned about with temperatures going so high. Metal expands slightly when heated, and contracts again when cooled. That could cause issues with contact, and over time metal fatigue could result in more serious issues (i.e. cracks). That's why you'd want a low difference between idle and load temperatures.
I don't think the Mac Pro chips are mobile chips, at least from looking at Techpowerup's GPU database. The desktop HD 7870 and Mac Pro D300 are both listed as Pitcairn, while the mobile 7970M (which has a similar core config) is listed as Wimbledon. Similarly the D500 and D700 are listed as Tahiti, which is what the desktop 7970/7950 are called.
But then I have doubts about the database's accuracy too. The D500 is clocked lower than the 7950 and has a more cut down core configuration, but has a TDP of 274 W - 74 W higher than the 7950's 200 W TDP. How does that make sense? I doubt that 20 MHz higher memory clock on the D500 is responsible for an over 74 W power increase. The 7870 XT has a similar core configuration (compared to the D500), but has an even lower TDP of 185 W.
I agree that AIB cooling solutions will be better in a large case with good airflow - my doubt is with whether the conditions in the Dune case will play well with open cooler cards.