You should have no problems with your AP mounted this way.
As a right handed, but left eye dominant shooter, who prefers to shoot left-handed, I just set up my new M3 with the on/off controls toward the left side of the GG&G Accucam Cantilevered mount (which is great, btw, and really the only way to position the AP in this mount), also.
After studying the Owners Manual for the AP and if I understand it all correctly (I believe I do), your windage adjustments in the left side turret are now reversed. That is to say your left side turret, as now installed, will indicate "UP-L" with the arrow pointing in a COUNTER-clockwise direction, however you and I will need to turn the dial CLOCKWISE to adjust our windage to the left, now.
The elevation adjustments in the topside turret will not change.
Read the manual for mounting in this manner and report back if you confirm or disagree, please. Inquiring minds need to know! Thanks.