It's a question that's been tossed about since the Caps claimed the 2015-2016 CONCACAF Champions League spot by virtue of being the highest placed Canadian team in MLS. It would figure, that given the Caps misfortunes (self-inflicted or not), that their initial foray in the CCL during the MLS era would be by a temporary amendment of the rules. After spending 5hrs in the car, to witness the gongshow that was the match that eliminated the Caps from the tournament last year, I'm glad that neither opponent they face this year is within a 5hr drive from Vancouver.
Lenarduzzi was very recently on TSN 1040 stating that the priority for the Whitecaps is MLS Cup.