The manual says

"One important thing to note however is that the tradeoff between time spent studying and retention is not linear: we can see here that to increase our retention by 5 percentage points, we’d have to study 35% more frequently."

This has nothing to do with linearity. The author probably meant instead that it is not 1:1. Just because the numbers are not the same doesn't mean it's not a linear relationship. Remember the function x is linear, as well as 5x and 17x. For the latter 1 step in x gives 17 steps in y, so a linear function without the 1:1 relationship. So you should probably change it to "not 1:1".

(Even though the author meant something different, the statement technically is correct since the log is a non-linear function. But graphing it in the relevant range one sees that it is very well approximated by a linear function: https://i.imgur.com/ZNRnTLe.png)