Thank you, any help on this matter is extremely useful.
Yes, the basics, like the respective encounter rates for the different world map regions, are in TF's guides.
However, even though I already know that the Junon Area has a 1/8 Mystery Ninja encounter rate, I feel this number does not mean anything at all.
As you probably know, field encounters are not random in the least (neither the "when" nor the "which" part), making it very easy to manipulate them.
Obviously, it would be great if one were able to manipulate world map encounters as well.
From the tests I have done using the same save file, editing different things via a save game editor, it seems to me that upon loading a world map save file, if one's movement on the world map is the same, only one's game time has an impact on when and which random battles take place. Interestingly, even altering one's world map location (while staying in the same world map region and not changing the types of terrain one will touch when moving) has no impact on when and which random battles occur.
Also, I have looked into trying to manipulate the Mystery Ninja encounter and have found some more game time values which allow me to get one all the time as long as I move only horizontally, never stop running or change the camera angle and end up getting the first encounter in a forest. Strangely enough, as long as I just hold Left, I can even deviate from the "only move horizontally restriction" and still get the Mystery Ninja encounter much more frequently than I should (35 out of 38 times using several different save files) as long as I don't touch the camera angle or stop moving.
Obviously, there must be some kind of "hidden" mechanics to this.
I know this may sound esoteric but, so far, I have found the following second counts that guarantee a Mystery Ninja encounter when abiding by the aforementioned restrictions:
3, 55, 59, 60, 259
I have not tried all the other values in between. More interestingly, I wonder if they loop. I would assume so, and 3 and 259 would suggest a modulo 256 repeating but 515 does not work. All the other modulo tests I have done did not yield any positive result either.
I have actually come up with this preliminary theory:
On field maps, the danger value is increased by a fixed amount per step (depending on the specific encounter rate of the respective field, and running increases it by four times as much as walking does). In order not to get a random battle on a given step, one has to pass a battle check on that step, i.e. one's danger value has to be <= (or is it < (?)) a certain not-so-random value that is taken from a look-up table and is determined by one's step count (mod 65536 (?)).
I assume the world map uses the same system. One's danger value is probably increased by a fixed amount per step (depending on the specific encounter rate of the respective region and terrain type, and one's camera angle might influence the increase as well). In order not to get a random battle on a given step, one probably has to pass a battle check on that step, i.e. one's danger value probably has to be <= / < a certain not-so-random value that is taken from a look-up table and is determined by one's seconds count (maybe mod 65536).
So, stopping one's movement changes what values are used as thresholds in the future battle checks.
Additionally, one never seems to be able to get world map encounters before either a certain amount of time has passed or a certain amount of steps have been taken (I haven't tested yet which of these it is).
On field maps, which encounters one gets is pre-determined as well.
On the world map, which encounter one gets seems to be worked out in a different way.