Why? Simple - because a top freediver, despite better O2 consumption and CO2 generation, is capable to cope with high levels of CO2 and bear with quite high CO2 levels. He/she is able to withstand the pain throughout until LMC or blackout. Top freedivers do not really rely on CO2 induced symptoms for aborting their breath-hold. They wouldn't be able to achieve a third of the time or distance if they aborted the breath-hold when they feel the first signs of CO2 induced discomfort. Sportive freedivers learn to recognize symptoms of impending hypoxia instead. Of course the CO2 symptoms are still important, but are so heavily influenced by different aspects (diet, breath-up, physical and psychical condition, ...) that relying on them at maximal attempts is simply not sufficient.
So while an experienced freediver is able to withstand many minutes of CO2 induced discomfort and strong pain, a non-freediver chickens out after the first few seconds of the slightest hypercapnic symptoms. And do not tell me that the CO2/O2 management at top freedivers is so good that after 10 minutes of apnea they have the same level of CO2 as a non-freediver after 30 seconds!
So yes, as I wrote already two times, the limited resistance to inhaled CO2 is partially explainable by the slowly climbing PaCO2 (alveolar partial pressure of CO2) after certain threshold, and also by different processes during apnea, and during normal breathing. But despite it, the result of practically no tolerance difference was surprising. Perhaps not so much for the lapse of physiological CO2 adaptation, but definitely it was surprising for the lapse of mental tolerance difference. And it was not only surprising to common freedivers without deeper knowledge of physiology, but it was surprising to the scientist studying the phenomena too.