I'm not sure what restrictions you may have but I can offer the following information.
While it is true that both conventional peening and flapper peening can be applied at the same intensity there is an issue regarding whether manual peening (i.e. flapper peening) is allowed. Most specifications do not allow manual peening unless stated otherwise. Therefore, my answer to you must be that unless you are specifically allowed to do flapper peening you would be required to perform conventional shot peening.

Also, for your information, the flapper peening is performed with balls of 1mm diameter (0.040inch). This would be close to a shot size of S390.

Hope this helps.