Marathon does not support task configuration template which can establish command patterns and avoid redundancy. We are trying to find a way around it, otherwise we need to create 100,000s tasks and it would be very difficult to manage those config files. One approach, we are thinking is running multiple marathon clusters inside mesos. Now the question is can we run multiple marathon clusters inside mesos? And is there a limit number of frameworks mesos can handle?
Yes, multiple Marathon frameworks is not only possible but actually considered a best practices. There are many use cases, from scaling to Chinese Wall setups (esp. in financial services area).
For example, in the DCOS we're installing a 'system Marathon' per default and you can then install as many 'application' or 'project' or 'group' Marathons as you like.
I'm not aware of a theoretical limit of the number of frameworks, but hey, this might actually be a good load test to run, I'll look into it.