I'm graduating in the spring and have applied to a number of PhD programs -- so, take my opinion with a grain of salt. I would say that depending on your profile that might be a very good decision, specifically if you're aiming for a very competitive school but don't have much research experience or have some weak grades (or limited math exposure). As long as the program is funded, it seems you have very little to lose. Additionally, if your professor suggested you do this that's probably because they know your profile and where people from your school get into grad programs, and they think it would be beneficial.
Needless to say, if for whatever reason you don't think it would actually help (or is the funding doesn't come through) then it might be wiser to go straight into a PhD program. But, it seems like a no-brainer to go ahead and apply alongside some other programs you have your eyes on.