Seems like the company would have to either misrepresent the job requirements/responsibilities/wage level (seniority).. Or perhaps they'd fake a survey of local wages rather than using the "official" statistics?
Otherwise I don't think the Department of Labor would/should certify an LCA with a wage way below market for the position. If they do, though, perhaps that's where the issue can and should be fixed?
In practice this also means that employers need to file an amended H-1B petition with a newly certified LCA when an H-1B employee moves to a new area code. For instance, if you move a H-1B software engineer from Denver to San Francisco you'll likely have to pay the employee more.
The article does point out that the issue was discovered by the Labor Department (rather than for instance the USCIS, who's responsible for processing the H-1B petition itself), so perhaps that indicates a failure to comply with LCA requirements?