Exactly right, you will figure out which holdovers work for your rifle/ammo choice. They may not match the manufacturers recommendations in the manual. That remains true whether you go with a 9mm, 5.56 or 7.62 reticle. If you change bullet weight or any other variable, the POI will vary and may not match the holdovers included in the reticle.
Even if you buy an optic with a 9mm reticle, as you change ammo type, the holdovers you were using at 100yards with a 115gr load will be different to a 124gr load etc.
Like Sniffer said, keeping good notes specific to your rifle/optic/ammo weight/brand will help you out down the road and save you a little hair.