Both of these commands do in fact use packager.json and cannot be assigned another json file.
For your setup you can simply use
sencha app package android.json
This will have Architect doing the first part (that you were doing at the cmd line before)
Then unfortunately you'll have to run the 2nd part (that Architect did for you before)
The reason for the change:
Many customers were trying to simulate and build using the local app directory and never doing a build first. This was very problematic as you yourself learned and resorted to a build of your own.
This change helps the less advanced user, that uses just one packager.json file and does the build and package in 1 step.
We are currently working on a much more powerful and simple build system that will allow you to have targets and different settings for each target. Example targets: build for android, simulate for iOS, build for web, etc ...
This will on the back end create a new packager.json file that Cmd can read depending on the target you chose and the settings you enter per target.
Sencha Architect Development Team