Yeah, while you do happen to be around to keep an eye on it, it can get kind of hectic with the bit of busywork it creates. (Kind of a cheap way to make the game more "engaging".) But that first haul when you log in after being away from it for several hours? Not denying that we're taking a hit there and it won't be good if you generally don't get a lot of time set aside for this one thing.
Hmmm... Saving up the kobans towards pachinko is more appealing of course, but at that kobans comment I could imagine someone setting up an autoclicker timed to space out the clicks just enough to spend 24 kobans on collections over a span of 8 or more hours (to farm it while you're either at work or asleep), or I guess just setting the autoclicker to stop after a certain number of clicks. Either way, you're only spending from the 25 kobans gained from completing all the daily missions. (And while you're getting each of those dailies done you can at least make sure you personally collect the cash as often as you can during that time.)
I don't know. It was kind of a bit of a hypothetical either way. People do have other things going on which make perfect efficiency with either system highly unlikely, or at least not something that can be kept up for long. (I think I saw a lot of timers working around 50-70 minutes now, compared to before where I recall a lot of them being more like 2 or 3 hours. Somebody who hasn't accessed the game in 8 hours will have missed a number of cycles with either schedule. And active play collecting (manually, to be koban-free) as the payments become available is obviously cheaper than wasting kobans spamming the quick collect often enough to get them as they become available and more efficient than hitting the quick collect with a slow autoclicker to collect in batches of however many finished sometime during the hour or so that you have it waiting between clicks on that button.)