There are a few ways to look at this. First with just the raw data from all competitions in which the Sounders face any of the 11 possible MLS Cup Playoff teams (both Conferences have a bubble team). Seattle Sounders FC have faced those teams 19 times this season. In those games they are 7-5-8 (WLD) with a +8 goal differential.
Three of those team the Sounders will face one more time before the Playoffs start. Against just Western Conference possible second season teams they are 5-4-4 with a +7 at an even better PPM of 1.46. Most of that has to do with great success against LA and Dallas, so there will be further tests and clarifications available soon.
One could also look at Sagarin's listing of performances against top 5 and top 10 teams. Seattle has a mere 1-3-2 record against the Top 5 teams. This is worst among top 5 teams and second worst among top 10 teams (Galaxy are worst). Expanding to top 10 teams the Sounders are 4-5-4 at worst and fourth worst.
By both of these measures the Sounders' performance against the San Jose Earthquakes sticks out as a major problem. That MLS only 0-3-0 -3 or all comps 1-3-0 -2 pulls down the averages. Dropping the best team in the league and Seattle looks good (so do all of those teams probably).
Are there worrisome dropped points? Absolutely. Are Sigi and Co. assured of another Playoff failure because of struggles versus quality teams? Absolutely not.