If I was to add a fresh chilli pepper at the end of cooking, how long in a simmer would you say before its been cooked(all unsafe things killed and it has released its flavour)?
If you want it to 'release its flavour' you need to either add it much earlier (with onions/ginger/garlic/whole spices) or make a temper to add at the end.
If it is a recipe that's suggesting you add 'at the end of cooking', then I'd say that's more of a garnish like fresh herbs, you should perhaps slit it but not worry about cooking it through.
If you do want it to cook slightly towards the end, then just slit and add as above, but wait for it to discolour and wilt slightly. By this point you probably have separated oil on the surface, so it can cook in that no problem say 2-3 minutes.