I am not aware of any exceptions to the law, unless you mean the Special Executive Service. You can - eventually - make it into the Special Executive Service (SES), which pays somewhat higher (around $200k per year, depending on specifics). But that typically takes 20+ years of service and is reserved to less than 1% of the total workforce of a lab or agency. It is extremely rare for someone to be hired directly into the SES, unless that person is a presidential appointee.
Which means that under ordinary circumstances, my lab cannot offer a Nobel Laureate more than $200,000 per year.
I'm not saying that there is no civil servant anywhere who makes more than that. But such positions are extremely rare. The Vice President only makes $240,000.
https://www.opm.gov/policy-data-oversight/pay-leave/salaries...
If you read the fine print, the executive order allows agency-level directors of the Department of Veterans' Affairs who are physicians to be paid market rates. That is probably who these people are.
This exemption doesn't appear to apply to any other agency or profession.
Also, that $995k for the CEO is just the base salary.. his full comp package is about $6.5m
It still might be challenging to get a decent raise short of leaving for competition though. Pay is very easy to address in the grand scheme, the work environment, the politics at many levels, the organization, the idea that you could and will go to prison if you were to violate a policy or blow a whistle, inability to talk with your spouse, peers, or even coworkers about work, etc.. those things are hard and they probably suck there.