I voted for the safety only. They would assist with the age old issue of riders on hot laps in qualifying, rain, oil, rider/bike down on the race line. Lapped riders? These bikes are nearing 350 klicks, physics can be a painful and sometimes deadly force.
Do not replace the flags though, do not make them compulsory, just an option for additional safety if desired by the team.
I would consider it to be against the spirit of motorcycle racing to have team to rider communication however. The rider managing his own race is part of the appeal of the sport.