But when one of the options is 10-99 status and the negotiations are serious (as opposed to the usual situation where the employer ofers and the employee says "yes" more or less automaticaly) it can be a factor.

I've had contracts where the client explicitly offered me a higher rate if I'd take 10-99 status. (And in case the IRS is reading this, it was legitimate - the other 10-99 qualifications applied, I set the hours and working conditions, used my own equipment, and in every way was operating as an independant contractor.)