You have limits for every user who uploads from your website right? Those limits are for IP. So, an user can only upload 100 images per day with a maximum 300 for month right? Ok, the API is not designed to be used by sinle peers or clients, is designed to be used by an application which is in the middle of the user and your server. So the API must have way more higher limits than the normal single user limits. By overwritting those limits in the file api.php you are just affecting those config values just for the API request, normal users will have the other limits.
So, is recommended that API has certain limits and users other limits. The API limits are for all those who use the API, if the API is used to pass images from one site or application, for Chevereto that is just ONE user even if the thing is used by 200 people because the request come from one single same IP. Got it now? API has shared limits, not individual limits.