So, $4k project, 12 days, used Photoshop, = $49/(12/30) = $19.60.
This would be hard to complain about as a client. For you, on every project you do, if you're a typical small design shop where net income is roughly 10%, you'll be adding 5% to your net income. Or, if you need two or three programs, then 15% to your bottom line.
Of course, if you're a freelancer, then you're adding $19.60 to your bottom line. But, I bet it would be nice to add those up, especially since projects tend to run long in days, not hours.