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To answer my own questions...
1. There are instance level settings for minimum (>= 100) and maximum application id. Judicious use of these settings along with the wwv_flow_utilities.minimum_free_flow API and manually deleting entries from apex_040200.wwv_flows_reserved until the packaged apps installer generates the desired id(s).
2. This one appears to be hard-wired into APEX. Manually updating the first_schema_provisioned column in the apex_040200.wwv_flow_companies table to one of the other schemas associated with the workspace seems to do the trick. The installer picks this schema both as the parsing schema for the app as well as the schema to install all the supporting objects.
Hope this helps someone else.