Blondie threw Tuco a shovel and let him keeping digging at the Stanton grave, full knowing that nothing was there, I think to flush Angel Eyes out. Blondie EXPECTED Angel Eyes to show up as the grave was being unearthed; Blondie shows no surprise when Angle Eyes appears, keeps 100% cool.My guess is that Angel Eyes was a couple hundred yards away watching everything play out, until he felt the time was right to appear. Maybe Angel Eyes was suspicious about that being the correct grave, or he likely would've simply shot Blondie and Tuco in the back instead of tossing a second shovel (and then being screwed when no money was in the Stanton grave).
There is one mausoleum in the cemetery he and is horse could have been in that, you see it during Ecstacy of Gold (I think it really functions as a camera set up)
Where could AE have been hiding?
A vast empty Western landscape. The camera pans across it. Then the shot slides onto a sunburned, desperate face. The long shot has become a closeup without a cut, revealing that the landscape was not empty but occupied by a desperado very close to us. In these opening frames, Sergio Leone established a rule that he follows throughout "The Good, the Bad and the Ugly." The rule is that the ability to see is limited by the sides of the frame. At important moments in the film, what the camera cannot see, the characters cannot see, and that gives Leone the freedom to surprise us with entrances that cannot be explained by the practical geography of his shots. There is a moment, for example, when men do not notice a vast encampment of the Union Army until they stumble upon it. And a moment in a cemetery when a man materializes out of thin air even though he should have been visible for a mile. And the way men walk down a street in full view and nobody is able to shoot them, maybe because they are not in the same frame with them. Leone cares not at all about the practical or the plausible, and builds his great film on the rubbish of Western movie clich?s, using style to elevate dreck into art.