The design of a PhD study is crucial to its success. The design process varies enormously according to the discipline. In the physical sciences, you are governed by the principles of scientific method. Study design may focus on detailed decisions about how you design your experiments and apparatus. In some cases, the contribution to knowledge may actually be in building an apparatus which enables a new experiment to be done.
In medical studies, the study design often involves selecting from a range of prescribed trial methodologies. Broadly categorised as randomised control trials, these methods seek to remove confounding factors by constructing an active group and a control group where the confounding factors would be randomly distributed across both groups. In reality, the student will need to identify the particular flavour of trial that meets the needs of their study.
In the social sciences and humanities, it is much less likely that a prescribed study design will exist and the choice and justification of your study design is likely to be a very important part of your study. I have met physical science PhDs from very respectable Universities who when asked “Why did you do your study that way?” would answer “Because my supervisor told me to!”. This is not likely to go down well in a social science context, where very often in my experience, discussion of methodology at examination time lasts longer than discussion of the results themselves.
From an examiner's perspective, it provides very good evidence of the level of understanding of the student, and givesconfidence in the results.