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Incorporaate making a Database to be created manually on Windows using the same Oracle tool (dbca).
Having a “smarter installer” is a valid enhancement request (product suggestion).
Start the Oracle/MM install with larger tablespaces.
What you request is a typical Consulting activity.
It is common to create the Database manually to have control about database size and location of the database files.
The OOTB Installation is more or less intended for demo or testing purpuses.
Alternatively, consider using SQL Server - there the whole Model Manager Database is stored in one file.