I agree with Nathan Knutson's comment that this looks like cable friction, but I suspect confirmation bias has everyone looking at the wrong portion of the cable routing.

The mechanic I spoke to said that this was a problem with the design of the Allant 7.4. The shifter cable comes out straight at the same angle from the chain stay. It gets bent upward and sits in contact with the quick release nut. The mechanic told me that the problem was due to the sharpness of the angle that the cable was routed after it exited the chain stay.

The rear derailleur cable routing isn't perfect, but it does not look that bad either. There is nothing inherently wrong with the cable housing touching something. The problem can arise if the housing is severely kinked, which doesn't appear to be the case, I beleive the manager is correct in that this is likely not the culprit.

You also said:

The shop I bought the bike from has replaced every single component involved in the rear gears (possibly not the external sheath at the back? The manager told me this couldn't be the cause of the problem). The cassette, derailleur, chain, shifters, shifter cable core (now using a thinner core) have all been replaced.

This still leaves a couple possibilities:

1. Cable housing from the shifter to the frame has a kink. You made no mention of whether or not the cable housing (cable outer) was changed. If the housing is a bit short and/or the handle bars get over rotated this can damage the housing. This however should have been obvious from inspection, and I would hope a reputable shop would have looked here first, long before cassettes, derailleurs and shifters!
2. Inside the frame, you are missing a sheath or the cables inadvertently became entangled during assembly. If the cables are tangled, then this would cause extra friction. You might be able to see this by activating one shifter and looking for movement on the other derailleur. Friction could also be increased if an internal sheath is missing. Most internally routed systems will run the cable inside a sheath to reduce friction. If is missing, then the friction is higher. The shop changed the inner cable, but depending on how this was done, they might have missed these type of problem (e.g., you pull the new inner cable through by using cable that is currently in place).

Typically, internal cable routing results in straighter cable runs and should provide better shifting for longer than external routing.