They dont need to get their permission. It is Nominative Fair Use and these things are done all the time.
If there wasnt fair use policies in place than even DSLReports would probably be in hot water for using so many registered logos/trademarks for so many different companies while bashing them for being such a failure to society and consumers.
Problem is, unless I missed it, I didn't see anything in the advert that explicitly stated that SodaStream DID NOT provide ACTUAL Pepsi/Coke products. This could lead to product confusion, meaning SodaStream was implying they were delivering actual Pepsi/Coke, just without the bottles and hence trademark infringement.
I guess then the burden is on Pepsi and Coke to prove your implications as I never once watched that commercial and thought they were providing a Coke or Pepsi product of any sort. But then again, I am probably brighter than the average American.