Goku and Vegeta had 1% of their powers inside Super Buu's body.

Daizenshuu TV Animation Parte 3 e Chozenshuu 3

*Buu sticks his head out of the wall of flesh. Moreover, inside his body, Buu is immortal. On the other hand, Goku's power is less than 1/100 of its original power.*

Tosh just cummed to this.

They were shrunken to smaller than fleas. So that makes sense.

This explains why they struggled against super boo, who not only was immortal but also had his full power regardless of his size. But even then goku as an ssj while being tired and weakened (1%) was doing more than just holding his own. He even states that he can kill him and boo was only able to survive it due to his immortality. Moreover, they were also fighting in the environment of boo's body, which also an extremely toxic place to live in. Where boo had full advantage, he could literally pop out from anywhere else. He even states how he could only tire goku out to absorb him which implies he can't beat him right away. Goku was also exhausted from his fight with the clones. It could be the case that the clones were also at their 1%. Since they had the same power as their real counterparts, who were already been nerfed due to being absorbed and they were relative in size to goku and vegeta. And notice how they couldn't increase their size unlike super boo's avatar which solidifies it even further.

So, the scale is:
SS Goku 100%>Gohan 100%>=Goku base 100%>Super Saiyan Goku 1%>Super Boo 100%>Clones 1%>Hypothetical Super Boo 1%.

Super Boo had 0.5% of his power when he entered his own body according to the legend of the Z legacy guidebook, and he still threatened Goku and Vegeta with 0.5% of his original power. Super Boo wins.

Seriously tho, why'd Goku plan to revert Boo back to fat Boo so they could win if the problem was the 1% mini Goku and Vegeta theory? That'd make them useless no matter the Majin Boo version. Like, I didn't even think much on it and I thought of an obvious hole that shuts down the inside boo power nerf theory.

Only in the anime.