I thought Twitter's API only gave you access to a small percentage of real-time tweets. Did Twilert obtain full firehose access or is another method being used?
However, the 'filter' endpoint gives you access to all tweets matching to your search, up to a certain limit. Unless you're tracking very commonly used words or brands like 'selfie' or 'ipad', you're likely to get all tweets you are interested in without ever reaching the limit.
cf. https://dev.twitter.com/docs/faq#6861
Also, the API limits are per authenticated user, not per app.