On the topic of the guide, its currently being stalled by data validity. By that i mean that a lot of the major online pokedexes have different values for the appearance rate of some many pokemon. I trust marriland more than sppf, so i asked marriland why i should trust his data instead of other online dexes. Once i have the source of the data, i will do the resources, then the guide. So i probably wont get anything to you for a while, because ill be doing the boring work of compiling route stats, and comparing appearance rates. But i will work on it!
Well here's my opinions of what happens in the game when you chain (very basic since i dont actually know the details).
When you reset the radar:
One patch is assigned randomly to each ring
The position of the patches determines the pattern-based part of the chance for the chain continuing. (The stuff you were talking about Eg. a pair = -10%).
Depending on the pattern chance, the appearance rate is taken into consideration to determine what patches contain the chained pokemon.
^ Thats kind of using the pattern/app rate relationship, and i do think the process is a lot more complicated than the 'thoery' i proposed.
This would explain the 99% pattern - the impact of the pattern is very high, therefore the impact of appearance rate is very low. If you take a 70% app rate pokemon, and a 1% app rate pokemon, and both have a 99% pattern, the sucess rate of the patch would be higher for the 70% pokemon, but only slightly, and very low rate pokemon can easily continue with the pattern. Eg [probably wouldnt be like this] a 70% poke could have 99.70% continuation rate with a 99% patch, whereas a 1% poke would have 99.01%.
So, what do you think of that theory (inverse relationship b/w pattern and appearance rate in patch determination)? Also BTW, you use the term 'made me questionate'. Its actually just 'made me question'. Another odd term in the english language.
I'm guessing there is a very complex formula that determines how many patches contain the chained pokemon, and which patches have the chained pokemon. To try and answer your question about 99% patterns, i will use some observations:
No matter what the appearance rate of the pokemon is, with the right pattern, the chain is heavily weighted to suceed if you go in the right patch.
When there isnt a pattern that greatly ups the success rate, the continuation of the chain seems to be down to the appearance rate of the pokemon.
*i kind of had a breakthrough feeling when writing this, probably like when you were at school*
What if appearance rate and arrangement of patches are the 2 dominant determinants of what patches contain? And they have somewhat of an inverse relationship? Eg When the impact of the pattern is low, appearance rate is a big factor in patch determination - and when the impact of the pattern is high, appearance rate isnt very pivotal in patch determination.