You loose awareness of the chair and floor supporting you, so you tense your shoulders and neck to make up for that. It doesn't help, mechanically, but it adds to the store of tension that you impose on your body as you work. There's a wonderful circular feedback loop between tension and awareness. When you're feeling uncomfortable but you think you've got to push on anyway, you tense in order to block out the uncomfortable feelings. Tension contributes to lack of awareness.
Lack of awareness contributes to tension.
Poor ergonomic design makes you uncomfortable and encourages tension and reduced awareness, which amplifies the mechanical strains imposed by poor ergonomic design. External factors include such things as workstation and equipment design, work schedules, and the like. Ergonomic analysis, by and large, focuses on the external factors, while work such as mine tends to focus primarily on the internal. These two classes aren't unrelated, because each influences the other, as noted in the previous paragraph. Both are important, and both need to be addressed to solve the problem.