Griswold, I think a big part of the answer is the wording of the statutory provisions, not just the fact that a retirement plan has a trust and is a taxable entity, unless it meets exemption requirements. The curse of qualified plans is that 401(a) says a plan is qualified "if" and then starts listing pages and pages of requirements that have expanded over the years, but never specifies the time period during which the various conditions must be satisfied. In the absence of Congressional guidance regarding the timing of all those "ifs," the IRS has interpreted as meaning "if [at all times and forever]." From whence, the necessity for EPCRS and its predecessors.
125(a), by contrast, just tells you that a participant doesn't have to include nontaxable benefits in his/her income on account of constructive receipt, if the requirements of 125 are met. That is by definition a time-limited requirement, since the only tax "person" with skin in the game is the employee, who has a 3-year statute of limitations.