Goku kind of admitted it, implicitly, to Piccolo, that he could have defeated fat Boo, but chose not to do so because of the new generation. It wasn't as blatant as him saying such later on to Vegeta, but to me it's kinda easy to read in between the lines. Piccolo obviously doesn't buy Goku's first excuse and phrasing of "I don't know" and asks why he didn't try until the end, asking whether it was because of the SSJ3 time limit. Then Goku smiles to Piccolo, which to me, although I may be diving too much here, indicates he could recognise Piccolo could read through him generally being the one to try until the end, and says he isn't supposed to be the one doing it (doing what? Defeating Boo)... And that he wants to test the new generation as a possibility for them to try themselves... That seems like a clear giveaway that he could do it, tried to hide behind the fact Boo is too strong (I couldn't do it), but when Piccolo presses him, he spills the beans, he's no longer from such realm so he shouldn't be the one doing that. The "nasty gamble" said by Goku may also play an important role in that --- instead of finishing Boo and ending the threat right there, he chooses to postpone the fight and put it in the new generations hands. It's a gamble because it's something that could be achieved sooner and ended right there, but he's betting on the kids, knowing their amazing power --- but the situation is risky overall, who's to say the kids while having a superior power won't act arrogant and give the enemy a chance like kid Gohan vs Cell? Or who's to say something unexpected may happen with Boo, like what did in fact happened? Even when the kids have the power on their side, which is what Goku emphasized on when saying that's why he wants to take the gamble ("it's a gamble but seeing those super gifted kids, I wanted to take it"), their personalities and unexpected things happening is still something he can't control and know for sure.
I think that things like Bootenks saying he's fundamentally different from the Boo back then doesn't imply Super Boo wasn't already plenty, just that the difference now is just so big that Goku can't hope to complete. He doesn't highligh either what exactly made him different. When Goku tells Vegeta "that's how Boo got so different", one important thing to remember is that Goku didn't know the specifics on what Boo did to turn into Super Boo --- he didn't observe that besides just knowing Boo's chi had changed. So he'd most likely harp on the obvious things he knows, which would also have a bigger impact emotionally wise to Vegeta, as he can mention how Bulma and Trunks were absorbed by Boo.
Even Elder Kaioshin saying "I don't think" seems more like a general way of saying they won't be able to do that. I don't always play too much attention on sentences such as "I don't think" as implying the result won't be so obvious because conversations are fluid enough in which a character won't always be outright clear with their words. More like a general way of saying "you are planning going there, Goku, but I fear to say there's nothing you can do". The fact Goku thinks they should go SSJ when fusing --- with Gohan --- having the fusion exceptional boost in mind, not thinking base could do it, should be also indicative that he thought of Gotenks Boo's power as from another order, not to mention how defenseless he seemed when Gotenks Boo was about to attack him, with him begging for him to wait a little longer --- 1st time I see Goku begging to his enemies lol.
