Is it a good idea to spend one year on a pre-PhD diploma to learn advance research methods?
I'm going to suggest that spending a year would not be a good use of your time. The end-all and be-all of doctoral education isn't the methodology, but using the methodology to do something interesting in your field. 

I would answer differently if you thought your background is weak and that you would only be accepted by spending this year, but with an MS that isn't likely true. If it were a matter of a summer spent on methodology then, again, it might be worth it. But a year feels like spinning wheels.

On the other hand, the course you suggest is in your field. If it can also get you closer to the research frontier in that field then it would have value for that, rather than methodology. At some point you need to cross that frontier so you need to approach it somehow. 

Of course, this isn't my field, and I don't know how difficult the methodology is, but I suspect that you can muddle through and pick it up - especially knowing that you have a need. It would probably delay your completion less than spending a dedicated year that might not even give you a benefit in your application.