Yes, twisted isn’t used by anything in Panda. You can comment out the definition in thirdparty.pdef. In fact you can remove anything in thirdparty.pdef that you don’t need.
The “stage” directory contains what you’d upload to a package host such as runtime.panda3d.org although if you only ever use it locally that isn’t very relevant.
Assuming I understand your question correctly, yes, if you want your runtime to pull its “images” and “coreapi” packages from the rtdist you have built, you need to specify the built_thaumaturge/stage directory via a file:// url as host.
There is no stage directory in the built_thaumaturge_rt directory.
packp3d is built as part of an rtdist, which was built with a --host flag. So packp3d itself has a dependency on a ‘panda3d’ package from some host or another, which I believe is used as default for other package references.
(I could be wrong and it might actually be using the host that the runtime was built with, I’m not entirely sure.)
Either way, when specifying a dependency, you can explicitly specify a host URL and version with something like -r package,cmu_1.9,https://runtime.panda3d.org or, if you are using the more flexible .pdef specification to create your p3d files, via extra arguments to the require() command.