In all honesty, counting sword tournaments / PTK / non standard tournaments seems like a weird thing to do as atleast normal tournaments are down to teams actual skill.
Take it from someone who doesn't like these formats (or at least nowhere near traditional formats) and considered for a while they were not as competitive (wrongly so though), I understand what you mean. The reality however is that it's impossible not to take these into accounts while making a competitive team ranking. Out of the last four tournaments we had recently, half of them are non-traditional formats and these events were attended by just as many competitive teams as regular gf tournaments.
I will probably have as much of a struggle taking the upcoming 9v9 into account. I don't mind MP hosting it, it's definitely a fun format but due to its size and the on-going summer vacations, I already know about three teams in the rankings who won't attend it (or if they do, that will be as a merge). It seems equally unfair to not take this tournament into account for the teams who are going to attend it with a strong roster, that it is penalizing those who don't.
Obviously moving forward we might adapt the formula and re-consider the tournaments we take into account (or consider if they are all supposed to weight the same) but I believe we will probably lean towards establishing a 'competitive size' (from 5v5 to 7v7 for exemple) rather than give more relevance to the traditional tournament (only bayonets).