The State Department recommends the same thing. However, as a US citizen, the State Department must treat you the same even if you have dual citizenship. Problems arise when an individual with dual citizenship [and two passports] gets in trouble in the country of his other citizenship. Then, US officials have a difficult time invoking consular rights and privileges, including visitation in prison.
FYI: I worked for the State Department for 28 years.
I certainly will defer to your knowledge of State Department policy. (BTW, did you work at State after 9/11/2001?) My practical advice, however, comes from four decades of travel to foreign countries and the harrowing experiences of friends and co-workers (both US and dual nationals) who have had passport difficulties (some admittedly their own fault) when traveling overseas.
In the case of the woman in the article who is a citizen of the US and who is applying for Romanian citizenship to obtain an EU passport, I would recommend that she use her US passport to travel between the US and Romania and then her Romanian passport if necessary for *work-related* travel throughout the EU. If she isn't working over there, then I would recommend that she use her US passport exclusively throughout the EU; once she enters Romania (or any other EU country) on the US passport she should have no problems traveling from one EU country to the other.