I think it will depend on how your product was sold to the customer.
If you only sell it in packages ...
PACKAGE 1 -> 3 reports, date entry, some other stuff.
PACKAGE 2 -> 6 reports, more stuff
PACKAGE 3 -> 12 reports, almost all the stuff
UBER PACKAGE -> everything
I would have thought it would be easier to set up a table of these packages and a link to it.
If you sell each module yourself with the changes ...
Customer wants 4 reports a week with an additional report every other tuesday if it a full moon.
Then I would ...
Create a table with all the product features.
Create a link table for customers and the features they want.
In that link table add an additional field for modification if needed.
CLIENTS
customer_id (pk)
MODULES
module_id (pk)
module_name (reports!)
CUSTOMER_MODULES
module_id (pk) (fk -> modules)
customer_id (pk) (fk -> customers)
customization (configuration file or somesuch?)
It matters to me the most.