Not sure I'm following you...the 17 round magazines are not M9A1 magazines, but come standard with the 92A1 (or the poorly named 90-TWO). The M9A1 comes standard with the 15 round PVD coated sand resistant magazines.
The yet to be released M9A3 uses 17 round PVD coated magazines, which are already available via the Beretta USA website.
However, all of these magazines are compatible across all Beretta 92 pistols. I've used the 17 round magazines in the M9 without any problem (well, save the floor plate cracking that I've documented previously in this thread). What may not be compatible are small parts across magazines - for example, as we were discussing earlier, the 17 round magazine floor plate will fit a 15 round magazine, but will not allow a 15 round magazine to seat properly. The reason is that the 17 round magazine body is actually slightly longer than the 15 round magazine body in order to accommodate the two extra rounds. This extra length is concealed by the shape of the floor plate.