I've been pondering this question myself. On a theoretical level, a HEPA filter is supposed to remove 99.99% of .1-.5 micron particulates, which are the ones we should be most concerned about. FestoolUSA says the SYS-AIR "provides over 99.9% filration"
However, when you look at the specs, there's not much stated difference. Both units seem to share the same Preliminary (1332 in2 surface material) and Main (3812 in2) filter. There is a price difference between the two replacement main filters, and the SYS-AIR HEPA has a slower cfm of 264.8 vs 423.
Sedge has been explicit in both the Festool Live featuring the SYS-AIR and in the Concord Carpenter video from JLC in Rhode Island this past weekend, that you cannot use the HEPA Main Filter in the non-HEPA SYS AIR because the unit is what controls it. Does this mean that the filters are the same but it is the airflow allowed by the SYS-AIR that makes the difference in particulate capture? Could it be that this is a case of two labelings but the same system? I don't know.
The page for the HEPA Main Filter does state that it is more efficient with 99.995% filtration. I'm interested to hear more from those who have been able to deploy them in the field. 200+cfm is pretty miniscule and in the Festool Lives, Sedge has placed the SYS-AIR next to the workpiece so that any errant dust from the sander is immediately sucked in. This may be the ideal use for the SYS-AIR since the cfm rating is pretty low. At 200+ cfm, I wonder how long it would take to truly scrub an actual woodshop.
If I were to buy one tomorrow, I'd probably get the HEPA - but mainly because I've become very concerned about maximizing air cleanliness in the shop.