1) to get to the warmer temperatures, you need to pass through the room temperature stage first. Things might change quickly, but not THAT quickly, meaning whatever is lurking in the soil can cause havoc/mutate/etc. before hitting it's upper temperature limits.
2) The areas where permafrost is generally found see summer temperatures generally at or below 'room temperature' now.
I do agree, that their tests could have been more thorough and included future scenario temperatures, but may underestimate the problem by not allowing mutation time.
I think they mean that the bacteria will not reach room temperature (20℃), but will get just warm enough to thaw out (1℃ or 2℃).
The reason they could die is probably not heat, but lack of anything to eat.