is it possible in Splunk 4.2.3+ to have separate Inputs, Props and Transforms per App?
App1: Listen on Port 10000, Extract Field foo1 only for the data from App1
App1: Listen on Port 20000, Extract Field foo2 only for the data from App2
Yes, these kinds of settings can be defined per app. You might want to have a look at this section of the docs: http://docs.splunk.com/Documentation/Splunk/latest/admin/Wheretofindtheconfigurationfiles
Ah, I see I misunderstood your question. No, the configurations are indeed merged. It is not possible to separate that per app - you'd have to use different sources, sourcetypes or similar.