My thoughts on this are just kinda taking every angle and assuming some things without a concise answer:
If Goku and Vegeta performed the fusion dance instead of fusing through the Potaras, how well would they fare Vs Boo-Gohan? Would SSJ be enough? Or would they need higher levels of SSJ? Or wouldn't even that be enough Vs Boo-Gohan?
For one side, we have Boo-Gohan commenting that, no matter if they fuse, they wouldn't be able to beat him. Boo-Gohan should be aware of the boost the fusion dance provides, having Gotenks as a reference and even more, now sharing their knowledge closer when they've all been absorbed. Though we don't know what level for Gogeta, Boohan had in mind. He knew Goku could turn into a ssj3, though that might not be guarantee a fusion with the one who just appeared there would be able to become ssj3. Though maybe Boohan assumed the worst case scenario... But also, he was going to kill them before giving them a chance to merge, so it's possible he still had his doubts and ran his mouth there.
Vegetto ends up stronger than Boo-Gohan predicted and even surprised himself with the strength. So I think Gogeta wouldn't be as dominant, if at all, with SSJ only. Goku was hoping to use SSJ to fuse with Gohan before he knew how amazing the Potaras were in terms of power. If he was taking into account a similar boost from the fusion dance, then it's also possible he'd factor him and Gohan fusing together and, perhaps, the boost being similar to that, with SSJ being enough to defeat Bootenks. It's a little uncertain though, because Goku saw how Shin and Kibito fused without the need to suppress their power at all, so would he expect Gohan to be at a level on par with how SSJ or would he expect his SSJ to just fuse with full capacity Ultimate Gohan? If it's the latter, then I don't know how Goku would base the boost they'd receive off it, as as far as he knows he calculated the power of the fusion via the two warriors with the same power. If SSJ Goku is a 10, Ultimate Gohan may be like a 1,000... Still, it may be possible that Goku thinks a 10 fusing with a 1,000 would be warranted, instead of his base, let's say, 1...
So what if previously take as an indicator that a hypothetical Gogeta would be ~ Boo-Gohan due to a fusion between father and son not being different may be skewed as Goku could not be expecting to fuse with someone equal to his SSJ, but join bodies instantly with someone >>>> his SSJ, which would likely produce a way more powerful warrior were Gohan to suppress.
There's the matter of the rival boost too that Gohan -- Goku wouldn't get, so if taking that as indicative that SSJ Gogeta (assuming Gohan suppressed = SSJ Goku) would be > Bootenks, then SSJ Gogeta would be >>> Gogeta as the rival boost, even though not being framed as the main reason, still has its share on their strength, which should affect a Gogeta fusion too.
But again, if Goku was expecting to fuse straight with Ultimate Gohan's power without this latter powering down, then he may be predicting a fusion way above a hypothetical SSJ Gogeta already. Who knows.
EML stated that a Goku Gohan fusion wouldn't be as strong as a Goku and Vegeta fusion. I don't agree with the statement, but supposing it's true, we'd have Vegetto > Gokhan... And then Gogeta > fusion Gokhan... But again, how strong would a fusion dance Gokhan be? We don't know...
... I think the fact Goku was already anxious to try fusion with Gohan, with the impending factor being Bootenks waiting them, shows it'd be enough to stop Bootenks. But which state would Goku then be thinking when knowing Gohan would need to power down to his level? SSJ3 Goku would be possible, as in, Gohan powers down to ssj3 Goku's level. So at least SSJ3 Gokhan (fusion dance) > Bootenks. If EML states a Goku and Vegeta fusion above a Goku and Gohan fusion(who'd be enough Vs Bootenks) then perhaps it's indicative that Gogeta could beat Boo-Gohan... In some state. And that one makes sense as far as fusion dance goes, since Gohan would have to power down to whatever level Goku would be in... So it's unlikely Gokhan could access Gohan's suppressed power. So a Gogeta fusion, since it also shares the rivalry boost thus stronger, would be also plenty Vs Bootenks and Boo-Gohan likely (though, I wouldn't say for sure the advantage of a Goku and Vegeta fusion would also be apparent as Potaras, I don't agree, as Gohan wouldn't need to power down). Unless, Goku was banking on the ssj3 to fuse with Gohan as a fusion dance but to couple with Boohan's statement, a hypothetical Gogeta (I think Boohan would assume the strongest state) would fall in between Bootenks and Boohan...
... Does Gotten and Trunks have a rivalry boost? I'd say they're rivals too... It doesn't have the same intensity as Vegeta pursuing Goku, but Goku doesn't pay THAT much attention to Vegeta, so it's more like an assymetrical rivalry... While Gotten and Trunks, even in a joking level, seem competitive with each others as kids. So if Gotenks also shares this boost, then Boo-Gohan could be also accounting it as the fusion's overall boost in his assessment, unbeknownst to him that the rivalry made Gotenks even stronger and just chalking that up to the fusion's boost in general.
Just rambling on and putting some thoughts here. There're a lot of variables here and it's really tough to have a concise answer on this, I'd say.