The following tweaks can be used to speed up your programming speed while using the Simplicity Commander -
Starting with a mass erase, either "commander device masserase" or as a part of the first flash operation ("commander flash --masserase <...>" is often a good idea, since this will run a chip erase which is a lot faster than doing the same via page erases. Both the flashloader and "commander device pageerase --region @mainflash" will use page erases, not a chip erase.
Either combining the images into one file, or simply flashing several files at the same time, would help, since it removes the overhead of invoking Commander multiple times. If the user use a .s37 or .hex file, there will be no extra blank flash programmed, since these files only contain the actual data to be written. Using a plain .bin file will generally not work. For example, if the user is writing data both to main flash and the user page, that would result in a 250 MB bin file, which Commander will refuse to create or flash.
Adjusting serial wire clock speed may help. The default in Commander is 8 MHz, which is the fastest the WSTK supports. If the user is using another debugger, such as a J-Link Pro, they may be able to use speeds up to 50 MHz.