I am organizing a multi tenant application with a single code base/application using subdomains to detect the tenant, then runs a SET SCHEMA on postgres to do the fun stuff.
Would a hooks + plugins setup meet your needs? ie: build the additional functionality into another model, on whatever actions you need to modify check a hooks table to see if the user requires any extra actions, hooks table also specifies the action to take so you could easily setup different configurations for different users.
If you found a better answer to this please update.