In the Programming Skills Challenge, it states that there are no cubes on top of the bonus cube. Are these cubes out of play completely? Assuming that they are, the total cubes available I’m seeing for this challenge are:

04 for preloading
20 in auto loaders
12 on the field, 4 clusters of 3
36 total

Yes, you are correct. The cubes stacked on the bonus cube are out of play completely and counting the 4 cubes for preloading there are 36 cubes available to a team in the Programming Skills Challenge.