I found this old thread <https://groups.google.com/forum/#!topic/google-appengine/lq92vUaKubs> about this same issue. Most of the ideas discussed are still relevant today, including the use of microservices <https://cloud.google.com/appengine/docs/standard/python/microservices-on-app-engine> and the ability to create a number of applications <https://cloud.google.com/appengine/kb/#create> under one account depending on a variety of factors like resources and usage history.
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