This amounts to nitpicking to the nth degree but I don't know whether the CBA says that. Article VI begins, "Individual Player salaries shall be those as agreed upon between a Player and a Club...." (my emphasis) and then it states what the minimum salaries are to be (increasing each season) and when arbitration becomes available (3 years as you say). It goes into infinite detail about what happens in split major/minor seasons, and meal money, and so forth. But I don't see where it says plainly that you can't "agree upon" more than the minimum.
Indeed, b-r.com shows Royce Lewis being paid $745,000 in 2024. The CBA minimum for that season was $740,000.
I somehow find this very interesting, even if totally unimportant. How in h-e-double-toothpicks did Lewis pick up an extra $5,000 from the Pohlads??? In his shoes, part of me would want to say, "keep your pity money, I'll get paid later in ways that will dwarf this pittance." The other part would want to crow, "look at me! I got SOMETHING."
But more importantly, what dark magic does Scott Boras use to pry a few dollars from the Pohlads' cold spectral clutches? And why does he waste it to get a mere $5K? (I know, I know: it's to show everyone he CAN.
Maybe most importantly, it seems to me that the players' association had to know this form of collusion among owners ("I don't have to pay you a penny more than the minimum, that's my 'negotiation' for you") would occur given the wording of the CBA, and chose not to include wording that either sanctifies the practice or somehow forbids it.