It's not just a matter of the fact that different markers have different dwell settings, requiring the actual dwell value to be changed - but some solenoids have different power requirements, and need different modulation settings in order to function well, but with minimum power usage.
Your dwell setting doesn't actually mean that power is supplied to the solenoid constantly for that length of time.
Normally the board supplies full power to the solenoid for a percentage of the dwell time. That is to actually switch the solenoid. The remainder of the dwell time is used to hold the solenoid open, and this often doesn't require full power, so the power supply during this period is rapidly switched on and off, keeping the solenoid switched, but saving some power in the meantime.
The specific solenoid used will dictate what percentage of the dwell time requires full power, and what percentage of the time can be modulated to save power. The actual percentage of each millisecond when power is on and off during the modulated period can also change from solenoid to solenoid.
Basically, if the board settings aren't suitable, you may be sending too much or too little power to the solenoid, and it could effect the function of the solenoid.