I must have better luck. In the last 10 years, I can only recall two instances where I had a 'stuck' bit that the operators couldn't clear. Once with RSView32, and once with Intouch. Both times, the HMI was set up similar to you except the buttons were still visible, but they didn't execute if the HMI bit was already on, or the device status correct. (its been long enough I don't remember the details). It may have happened at my plants more that twice, but when the HMI allowed the operator to click on the buttons and get things back in sink, and unstick the bits, I didn't find out there was ever a problem.
One other reason I don't like to see the PLC clear bit set by the HMI, is like you said. It makes troubleshooting harder. If the PLC turns it off, I can't see that the bit comes on if it's turned of with a one shot, or I have to be quick if it is from a timer.
I prefer to see that the HMI start latches a PLC start when the HMI start turns on, and the PLC start turns off when the motor starts, faults, or the HMI start turns off.