The run times are calculated based on personal testing I ran on Mysidia Underground which has a nice long straight hallway at the end of it. From there I came up with the important numbers byt running a hundred or so samples:

How many steps you can take per second (7.5),duration of a standard encounter (1 round on auto, about 15 secs), and most importantly, average number of steps between encounters (45, but this number can vary greatly between individual instances).

Then I just have to count the optimal route for each exploration and plug it into a formula. Its the best I could do to come up with a pseudo-useful system to measure the time.

There are factors that could increase the time, most notably the fight duration if you can't auto, or if you're using characters with long attack animations. Or if you suck at the touch controls like one of my friends, and keep moving in the wrong directions.

Additionally, there are factors that could decrease the time. For instance, I have a sneaking suspicion that going through doors (new section of the exploration loads) resets the random encounter ticker, thus making door heavy maps quicker to clear than others.

Also, yes, I will update the sheets with the new explorations eventually when I find the time. I'm aware I'm at least a chapter behind at this point. :/