Right now, i have my doubts about whether or not Goku was using his full power against Fat Boo, but i think he was using his FP.
What puzzles me is this statement by Piccolo: “Goku…There’s something I want to ask you while I’ve got the chance…[ ] …That Super Saiyan 3 thing earlier…if you had gone all-out, wouldn’t you have been able to defeat Majin Boo?
The underlined part is a bit confusing. There are two options;
Option A - Goku was using his full power but was not trying to kill Boo, which is why Piccolo says "if you had gone all-out'
Option B - Goku wasn't using his full power against Fat Boo.
I go with Option A.
It is also possible that Goku has two full-powers;
A; His normally accessible full-power, which is what he uses against both Kid\Fat Boo
B; The power he receives when he gathers ki for 1 minute, which is what he was planning to use against Kid Boo.
I think this is plausible.