Well, there are people who would say the same thing but in reverse. There is a rationale behind that, even if I think it's wrong.

I don't think two-boxers think they can fool an omniscient super-being. They do think that whatever is in the box cannot be changed now, so it's foolish to give away $1,000. Would you one-box even with transparent boxes? If not, then you understand this logic. There's a reasonable argument there, especially as in the original paradox Omega is not perfect, so there's a chance that you'll get nothing while passing up $1,000.