Yes. NationBuilder supports multiple donation pages and separate bank accounts, where you can clearly mark whether a donation is tax deductible or not. NationBuilder also allows you to create separate public web sites on a single database, and to use database tags to denote whether a supporter is part of your C3 or C4. You can then run queries on those tags to see how many of the people in your database are within each type of organization.
If your legal department insists that your databases must be totally separate, you can use multiple NationBuilder accounts, but it is within standard non-profit practices to segment IDs within a single database. If we can be of help on this issue, please let us know.