This system was obviously dreamt up by some statistician on steroids as it is far too complicated for what is a simple sport to understand. I'm taking the Men's marathon as an example here.
FACT - max of 3 per country
FACT - 2:11:30 gets you a spot PROVIDED your country selects you
FACT - max field size of 80 (not 100 - oh, and those silly doped up run-walkers have a field of 60, like wtf and who actually cares!)
So at the end of the qualifying period we end up with a big ranking list including more than 3 per country. Keep in mind that the list may not actually include some of the sub 2:11:30 guys if they have only run one performance - it's possible and if your country doesn't have the competition for 3 spots then why not secure the standard and then rest up a bit before training your bollocks off.
But to make things easier let's just assume the ranking list does include everyone. So the IAAF will release a 3 per country ranking list. This is the baseline ranking list and does not mean these are the 3 (up to) athletes that will be selected for that country. For someone like Kenya then surely they just pick the 3 they want as they will all be sub 2:11:30, same for Ethiopia and for other countries - if they have more than 3 time based qualifiers then they pick who they want from those time based qualifiers.
It gets murkier when we move to the rankings list. The catch with the rankings is that if you are in the top 80 and you are not selected by your country then your country is potentially giving up that spot and the next available spot on the list is available. Eg if you don't select your 3rd athlete who is ranked 68th then I guess you can select your 4th ranked athlete assuming they would insert into the rankings in the top 80 (your 3rd and 4th ranked athletes may be 68/69 but obviously the 4th ranked guy doesn't show up on the 3 per country list - remove the 3rd guy and he slots in at the same number).
If you don't have another high enough ranked athlete to fall into the top 80 then you lose that spot to the 81st ranked athlete from another country (was 81st, now 80th). It depends how the list is updated if someone isn't selected and it makes sense to just take that one athlete out of the equation and recalculate. If you have a backup athlete for your country then great. If not then you are giving up the spot. I don't think it is right that your country earns say 3 spots on the ranking list then you can send whoever. That "whoever" still has to be in the top 80 once it all comes out in the wash.
If we go back to Rio and if you remember the Road to Rio rankings list where the upper portion was the list of 3 per country and then the lower portion was every other "qualified" athlete (or "also ran"). The 3 per country was based on fastest time and countries didn't always select the fastest athletes, so as the selections went on, the list was updated and sometimes an athlete would go from the bottom "also ran" list to the selected list. Others would also drop off after the country made its selections. The drop from top list to bottom list is what I'm getting at above but I've not seen how this will work going forward.
One thing to remember is that some countries are notorious for not selecting qualified athletes due to their own self imposed tougher standards. It seems some people now think that just because there is an official ranking and you appear in the top 80 then you will get to go. Those same countries will still impose tougher standards which will now be worded around world ranking spot ie must be top 30/40/50 in the world ranking. Along with injuries and doping bans (!) this means that guys in the top 90-100 still have an outside shot of getting to the magic 80. But you won't have a frickin clue until about 2 months out!