He's right, I'm not sure why this is difficult to understand.
Right so there's a few issues with this line of thought. For starters, Primal Groudon might not want to stay in on Rayquaza anyway; Draco Meteor is common enough and Primal Groudon is valuable enough in most given matchups that it might not even want to stay in on an unscouted Rayquaza, and if you reveal Surf as it switches out then the move's gonna be useless for the rest of the game (not to mention the fact that it's likely gonna hit the opponent's Rayquaza switch-in for very little damage anyway). Of course there are exceptions to this but if I see my opponent switch Rayquaza in on Groudon and I have a decent Rayquaza switch-in then I'm not gonna wanna stay in with Groudon, anyway.
The next issue is the opportunity cost of Surf; I've said in the past that Rayquaza wants all of Swords Dance / Extreme Speed / V-Create (or Fire Blast) / Dragon Ascent / Earthquake / Draco Meteor / Outrage but it can't fit all of this, leaving very little space for an eighth possible coverage move in Surf. Extreme Speed and Dragon Ascent are already mandatory on most every Rayquaza, so in the last two slots you want something to fit your team's needs best and if you feel like you need Surf on Rayquaza as a crutch to compensate for Primal Groudon, then there's either a massive underlying structural issue with your team that needs fixing or you don't need the move nearly as much as you think you do.
Finally, I find it interesting to note that while Primal Groudon is the most commonly used Pokemon on the ladder, it only had 50% usage in week one of SPL, and it's important to note that SPL is generally the leading factor that shapes a tier's metagame. If any of the opponents of some of the best players in ORAS Ubers (Jibaku/Evuelf/Edgar/Steve Angello/Donkey) used a Surf Rayquaza (nobody actually used Rayquaza in w1 of SPL but that's kind of irrelevant), it would have been a total waste of a moveslot. While Primal Groudon "sun" is definitely the most common playstyle among the general community right now, it stands to reason that once SPL ends and the meta settles down that Sand/Primal Kyogre teams will almost definitely become more common (though admittedly I find it unlikely that they will eclipse Primal Groudon teams in usage, the point I'm making here is that there will be even less of a use for Surf in the future).
This is like running Waterfall on Primal Kyogre to 2HKO Blissey, but maybe even a little worse. You're running a weak Special move with a single target on a Pokemon with Choice Band (if you use Surf to finish off Primal Groudon with your Choice Band Rayquaza then you're setup fodder for legitimately everything commonly used on offense, and have fun breaking Primal Groudon stall used by a half-competent player with Choice Band Surf). It's a little more acceptable on a Life Orb set, but if even you admit that it probably isn't 100% viable then it doesn't deserve a mention anywhere except the OO section of an analysis, if that.
This is 100% irrelevant and I don't know why you'd bother mentioning it. tl;dr, and I'm sure I've mentioned this to you before: lurk more, toshhy.