Well there is video of his fights in MMA, at least the striking aspect is clearly shown there. So they could used it as a basis for them to gauge how good Ngannou will be as a boxer. For me they really underestimated him as he is a MMA fighter. And I do think that Fury is just saying post fight that Francis is good or even a difficult fight that Usyk (obviously he is down playing Usyk here).
Nevertheless, its a rude awakening for the champion and he is very lucky that the judges give him the win here. I know that there is a continuing debate as to who win this fight. But it's clear to me that Fury didn't prepared or trained very hard in this fight, he is just saying that he did after the beatings that he got so somewhat stroke his ego and not to hurt.
Doubt that this Ngannou mma career would be a good basis to evaluate his boxing. First of all octagon is much different from the ring. Ropes vs net, obtuse angle vs right angle, gloves difference. Difference in fighter movement is to much to take it as basis. As of you would compare ice hockey and bandy. Same stick+puck+skates, yet two different games.
But isn't it that is the basis why we put him as a huge underdog in this fight? He was supposedly just like any other MMA fighters, they are multi faceted and boxing or at least what they call striking is not Ngannou's strong suit, he just had a power but he is raw and that's it. But everyone was surprised by his performance against the best Heavyweight in this era, he knock him down in the 3rd round and almost pull an upset.
However, I would agree more to you saying that Fury did not properly trained for the fight, than he underestimated his opponent or Ngannou was to good for him.
Probably Fury didn't trained hard enough and he should now what is the consequences of it. So I do not believed it, maybe this is just an excuse on his part because he was almost beaten, or for some he lost to a supposedly MMA fighter with no boxing skills.