Hey Ingo,
Yes, installing dependencies on each container will affect deployment time along with disk storage and CPU / RAM to one extent or another, so should be considered carefully.
As far as the GAE services in the context of a Flex app, the JVM, python environment, golang libraries etc. in the Flex context will connect to the services by their own means, presenting the same surface to user code. Each runtime is slightly different in how connection to App Engine APIs is provided and which APIs are available, and you should check
this docs page as the starting point of an investigation.
As far as services operating above the instance level, such as HTTP(S) load balancing, versioning, traffic splitting, per-version domain names, Cloud Debug/Trace, logging, and the rest, these operate in a similarly-transparent way, often requiring no extra work or tuning, although the underlying implementation details are of course distinct and there may be some differences here and there. The documentation is a great place to start, and if more concrete questions come up, don't hesitate to post them! It would be hard to list all aspects of each of these services, so I hope this high-level comment is sufficient to give a picture of the parallel-yet-distinct nature of Flexible and traditional environments.
As far as GCE purely considered and
Container Engine, these are much more toward the traditional web-server model than App Engine is. You're basically provisioning virtual servers which can run web-server software or any other kind of software. Container Engine is a higher level of abstraction than individual VMs which allows you to provision and manage fleets of VMs (not usually that useful for startup apps, but becomes useful with scale). Within a python process on a GCE VM, for example, one can still interface with Cloud Platform / App Engine APIs using Google API
client libraries or the Google Cloud
client libraries more specifically, but the autoscaler, versioning, etc. of App Engine are not available, although there are Compute Engine parallels, such as the
HTTP(S) Load Balancer.
I hope this has been helpful, let me know if you have any further questions!
Cheers,