A Change order is a shared contract change. It's the legal amendment of the contract to reflect the changes made to the work.

A Design consultant is not writing the specifications per se (assuming we're talking about Civil projects and that there are no special specifications). What happens, as you've pointed out, is that we're conforming the drawings to the agency's state specifications. These will change agency by agency with a lot of overlap. Sometimes the DDC will use the NYSDOT's specifications and vice versa.
Why re-invent the wheel. This is all public domain as well, there would be no need to write a specification unless the drawings require special specifications.

I've only every work for Civil construction, we would never be expected to write specifications but more to conform to their state issued ones.

There's too much bloat in this industry. I come from a scientific background. I tend not to accept 'that's just the way it is' as we continue on an unproductive role. Something has to change in the lowest bid sphere.

Of course there's Best Bid and Design-Build which seems to be a step in the right direction, but it comes with its own set of special failures.

I'm rambling at this point but just to summarize, yes you're absolutely right. Contracts are written for the contractor to conform to their specifications, which opens risk to the Owner when their specifications can not be met.