Hi passionate4nature,
I think the first thing I would try would be to remove the Chilipad for a night or two just to confirm that this is what is causing the issue in your shoulder blade or upper back.
If it becomes clear that the Chilipad is the issue and your shoulder blades and upper back are fine without it, I think the next thing I would probably try is to use the Talalay layer on top to see if this makes a difference. Talalay will generally feel softer than an equivalent ILD of Dunlop and this may make some difference.
If this doesn’t work, then I would first experiment with the Chilipad under the Talalay. It is more breathable than Dunlop and may allow the cooling effect to come through a little more effectively. You could also compare it to doing the same thing with the Dunlop to see if it makes a difference.
I have no personal experience with a chilipad so I don’t know how well the cooling effect would go through the latex but it seems to me that is should have at least some effect even if it’s reduced by the latex which would insulate you from the cooling to some degree.
Any condensation won’t hurt the latex directly but it could increase the humidity levels inside the mattress which could create a more friendly environment for mold or mildew or dust mites so I would monitor it and make sure that you let it air out from time to time if it appears that there is any condensation happening inside the mattress.
As you mentioned the tubes are another issue that would need to be resolved. Perhaps you could place it so they could exit from where the zipper closes if you leave it open slightly so you don’t have to cut a hole in the mattress?.
You could also try a mattress pad or thin foam or wool topper to go over the chilipad if you think this would isolate you from the feel of the Chilipad enough although the more you put on top of the latex the more it will affect the feel and properties of the latex itself.
Another possibility may be to use a thinner mattress cover (9") and then use the top layer of your mattress as a topper over the mattress (you would need a separate cover for the topper as well) so the tubes would have a place to exit from under the topper. I would confirm first though that the cooling will go through a layer enough to make a difference though before making more radical changes.
You could also use a 3" layer of firm polyfoam as the bottom layer in your mattress and then buy a 3" topper cover just for the top layer to make a topper over your mattress (you wouldn’t need a new cover this way).
Of course you could also poke a hole in the mattress cover but I would be hesitant to do this because I don’t know if the hole will “grow” over time. Before considering this I would sleep with the cover unzipped for a few nights so there was a place for the tubes to exit without making a hole and you could test how well the Chilipad worked under a layer of latex.
That’s about all the potential solutions I can think of … at least for now 
Phoenix