Secondary Research Questions in a Master Thesis, where to answer?
I agree with your supervisor about the positions for the questions: Those should be in chapter 1. Answering the question about the position of the other questions is difficult because we now neither your work nor the questions.

But the answer in chapter 1 as well seems to be odd - I would assume that those could be a result of a state-of-the-art analysis (in your case chapter 3) or of the "Results". 

But maybe those questions are not really research questions but sub-tasks you have to do in order to achieve your goal. Then the "Methodology"-chapter would be appropriate, but I would not list them as SRQs but as "tasks".

In the end, readability should be considered, too. 

Finally, your advisor is grading you - and if (s)he strongly suggests one option, I would follow the suggestion. But I would show my "optimal" solution, first.