Complete guess, but I would say they weren't just optimizing for ease of creating software, they were also optimizing for ease of creating the hardware.
If you're creating hardware that's only going to be used a few times, it's probably not worth it to spend a lot of effort into giving it every feature that programmers want.
I think you're on the right track but the motivation would be more for a smaller, lighter mass computer and not so much the one off nature as they made many hardware changes as requirements changed.
Still I feel the 1s compliment was perhaps more of a choice based around the familiarity of the designer, Eldon Hall. It was a style of the times and 2s compliment had not yet become the dominant standard.
If you're creating hardware that's only going to be used a few times, it's probably not worth it to spend a lot of effort into giving it every feature that programmers want.