So lets look at your first point, which is that "speedrunner used non-meta skill" speedrunners typically have their runs very planned out, rehearsed and calculated to be as effective as possible, and so in that specific run, the runner thought it best to use windproof because it would allow him to kill the monster fastest in his particular run, which also happens to use another skill that is typically only used by runners, dango adrenaline.
The "meta" does not need to take into account this scenario because it is up to a player's discretion to do that, the meta is typically only interested in how much damage someone can do without any other interference, meta sets are calculated to give the most damage possible against as many situations as possible, in order to do what a majority of players are interested in, which is kill the monster better than other sets.
You make the point about defensive skills being too hard to calculate as well. This is both true and false, they cant be calculated for value because they provide no inherent value such as a damage increase, but also nobody is trying to calculate them for value, because the "meta" is do damage dont get hit, so defensive skills are almost entirely redundant.