SM Minato was logical since it was hinted by Pa, only the introduction was weird. No-eye Madara was the asspull
Pa did imply Naruto was better however. But many people quickly came to the wrong conclusion that being batter was related to the natural energy balance. I think however it was more related to the amount of natural energy one can draw inside the body. Maybe Naruto pulls in far more natural energy at once than Minato or Jiraiya are capable of. That's a thing, too, in this manga. Sometimes there's a different level of mastery that is understood, but not necessarily always spelled out for you. Fukasaku seemed genuinely impressed with the sheer quantity of natural energy that Naruto could pull in.
Minato was also a toad contractor and not a random toad contractor. It was the Fourth Hokage for god sake, one of the greatest ninjas Konoha has ever produced, a once in life time genius.
As for the arguments around why he wasn't mentioned by Pa during Naruto's training, it's not the first time we see this. The Third knew everything about the First and Second, and yet he conveniently left out that Tobirama was the one who created Edo Tensei in part1 during their fights. Even Tobirama himself didn't mention back during the fight against the Third that he was the one who invented the jutsu. Information being left out isn't proof of your claims. You need direct evidence to totally contradict what we've learned, and even then it's possible for certain characters to not be fully knowledgeable on all the facts, such as Naruto believing that it was his father who invented Hiraishin.
Not just Fukasaku's words, but Gamabunta's also. Why specifically would Naruto in Sage Mode remind him of both Jiraiya and Minato? Why not just Jiraiya himself, since Jiraiya is suppose to be the only human to have ever achieved Sage Mode? What relevance does Minato even have in that situation. Why bring him up at all? Where is the connection to Pain, the Rinnegan, Nagato, Jiraiya's previous battle with Pain? The connection is others who have achieved Sage Mode. Pa probably has good reason to believe that Naruto's mastery of it has surpassed those who came before him. It isn't a case of Kishi saying "Hey, look, he must be Naruto's father!" Nope, that wasn't the point either.
Naruto surpassing his predecessors can mean a number of things. Simply having become a true Sage doesn't place Minato's mastery on the same level as Naruto's like i've explained above. That's like assuming all people that hold the Rinnegan or the Mangekyou Sharingan should display similar power and mastery. We even just recently learned that the pattern of your Mangekyou Sharingan enhances specific abilities