The rationale, is this is the best algorithm they could come up with. It's yet another loophole similar to how return GO trips downtown are free or very cheap if you start your final leg in under 3 hours.
If you follow along, you'll see that the general level of expertise at Metrolinx in most areas is very, very, low. But I give GO credit for at least putting a working calculator on the website that follows the same bizarre rules as the machines do!
Perhaps this is why there are no Presto readers on the platform - to avoid the temptation of people jumping out at every stop, and tapping in and out (wouldn't work because of the delay in allowing to tap - but I have done similar at Union, when I boarded at Exhibition and had not had a chance to validate my book-of-ten ticket ... so used the 6-minute stop at Union to do so ...!).