I looked at the paper. I don't really like muticentre trials precisely because of this problem (methodology differences) and their attempt to reduce bias, which actually introduces further bias. However, I believe there is no problem comparing the two treatments, even though they differ in duration, since the variable considered is time to treatment failure. The protocols are different, but failure is defined the same for both treatments i.e. platelet count < 30 x 10^9. Next time, they should plan for equal duration of trials, use one facility, examine treatment success, and maybe not publish in open access :)