There are no real disadvantages to it if it is set up correctly. You will lose a little average amperage when the pulser is turned on but that can be offset by turning up the main amps.
If welding real thick stuff, you may lose some total penetration and you may need to up your background some.
The background should never be higher than the peak or equal to it for that matter. If it is, you are not pulsing between different amperages.
What materials and thicknesses are you running?