Let's ignore that they're crap.

Person A believes they work.

Person A says "we shouldn't use this on Persons B, C, D".

Pretty major implications about the integrity and suitability of Persons B, C, and D, and about how Person A suspects they have stuff to hide.

(In some ways this is a good reason to keep them around. Even if some people know they're crap, the existence and popular mythology causes people to reveal more than they otherwise would through actions like this.)

If they were using dowsing rods instead of polygraphs would you still feel the same way?

It’s certainly suspicious. But it’s also a huge problem they use them at all when the private sector was banned from doing so since they’re so unreliable decades ago.

I think that's one very reasonable interpretation. The other is "I really want these people w to come work here and they don't want to do the polygraph because it's a huge pain so I as the manager I'm going to waive it to reduce their objections to being hired".

That's something that companies do all the time, they pay people "out of band" or give them extra benefits or accelerate their vacation accrual or vesting, or one of hundreds of other things.

I agree it looks bad for sure but it isn't necessarily sinister.

There has always been a contingent of people that do sensitive work for the government because they have important expertise but are either "unclearable" or unwilling to go through the formal clearance process. Limited affordances are sometimes made in these cases at the discretion of senior officials with that authority. For the government it is a practical risk/benefit calculus and they still have the ability to do a substantial background check on their own without a formal process.

While it would never be allowed for the average Federal employee it does exist outside of purely political positions.