An important reason is that Antarctica is much drier than Greenland and so snow accumulation is much slower: for the same thickness of ice the total time involved is much larger at Antarctica. Another factor that may be important is the partial melting of the Greenland ice sheet during the Eemian (see papers on the NEEM ice core).
Only the Antarctic ice sheets go back to the Eocene-Miocene transition 34.0 to 33.5 Ma ago. The NH ice sheets formed at the Pliocene-Pleistocene transition 2.6 Ma ago, when CO2 was below 300 ppm and the Isthmus of Panama had closed. See:
The reason that Greenland record is less than Antarctica is that the ice cores from Greenland only go back about 100 ka, possibly because the most of the Greenland ice melted during the previous inter glacial.
The paper you cite is available here: Article New results from ODP and IODP on the greenhouse-icehouse tra...
It is a review of a paper by Tripati et al (2006) which is also included at that site.
Note that your snippet " As in the earliest Oligocene, the [late Eocene] isotopic data seem to require the presence of ice sheets on Antarctica at least as thick as those today, and substantial ice sheets in North America (most likely Greenland)" is followed by the sentence "This latter result runs contrary to conventional wisdom, which holds that the Northern Hemisphere glaciation began tens of millions of years later [ Driscoll, N. W. & Haug, G. H. Science 282, 436–438 (1998)].
Tripati et al base their belief that there was a NH glaciation on the change in depth of the CCD, but that depth change in the CCD may have been due to a greater amount of ice in Antarctica than in the dry condions prevalent today, or a change in ocean chemistry. I am not conviced that the NH glaciation began before the Pleistocene.
800 ka is when the glaciations changed their frequency from 50 ka to 100 ka known as the Mid Pleistocene Transition. But this is explained in the Introduction to "Interglacials of the last 800,000 years" here: Article Interglacials of the last 800,000 years
Lack of atmospheric CO2 is not the only thing that can cause ice sheets. Altitude and Latitude also affect the snow line. Thus your missing ice mid latitude ice sheets may well be in the Himalaya, Earth's third pole.
Greenland would have been much warmer for most of the Cenozoic than how the Vikings found it. There is fossil evidence in Ellesmere Island for crocodiles etc, but in Greenland most of that evidence has been buried under ice or eroded away by ice sheets.
It's useful to clearly note the distinction between the age of the ICE and the age of the ICE SHEETS. The age of the oldest cored ice is about 125 and 800 kyr, respectively for Greenland and Antarctica, and there may not be much older ice, because of the slow lateral movement of the ice sheets towards the sea.
The age of the ice sheets as entities is much older, probably going back to the Oligocene for Antarctica and Pleistocene for Greenland (with or without periods of full deglaciation).