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I think that having the other revenue sources transparent to the users would help both problems. People do want to know that a service that their business depends on (even a little bit) is going to stick around, and they don't want surprises when you ask for money from something other than subscriptions.
If the revenue is coming from transaction fees, present that as a feature. I could really see a transparent transaction-based model with free accounts working.
When you say "invoicing should be free", that sounds like a nice revolutionary pitch, but I wonder if BallinBige could clarify what features would be paid?