"To think out of the box" significa ser innovador, tener unas ideas fuera de lo común. Así que supongo que se refiere a que la forma de administrarlas es más bien funcional, nada innovadora, convencional.
Excuse me responding in English but it is a difficult expression at my level of spanish.
First point: the original phrase is terrible jargon, and therefore poor English. "'Out-of-the-box"' would usually be hyphenated and means outside the current parameters. "Non-out-of-the-box" means the opposite, ie within the current parameters.
So what the phrase means is the the thinking is linear (ie straight-forward traditional and analytical) not lateral (ie dynamic, creative, and innovative).
Basically it means the thinker did not come up with any new way of looking at the problem.