Ok, to answer your last question, if you look for a flawless spread (ignoring nature) you'll get a flawless gyarados, ID and SID don't matter for that, they only determine the nature and gender of the red gyarados.
An example:
I want my red gyarados to have 31 in every stat so I plug d2140289 as seed in RNG reporter. Method 1 frame 114 says that I'll get a timid female one.... but I want to check out the right method, Chained Shiny, which says that I would get a male Relaxed flawless gyarados on frame 101 because my ID is 06627 and my SID is 39326.
Basically, you need to find a spread that will have the right nature for your ID/SID combo on method "Chained Shiny".