We have a custom Home tab where we placed the "custom check in" icon. We kind of discourage going to the file tab unless absolutely necessary by making selections available elsewhere.
We found the same challenges Ben describes so we decided to use custom only.
With the Automatic Checkin, aside from not writing the viewables, failures are not easily recognizable. One has to verify all is good before moving on. Errors are sometimes not easily identified so one ends up spending time looking around to be sure. Since we are taking time to "making sure", it was decided to spend the effort using the custom side and then all is clear and straight forward and is done once.