Hello Dan,
Yes, the original stereo SEX amp had some deep bass limitations that came primarily from the Speco output transformer. This was greatly improved by the Magnequest output iron, and later by our own in-house designed pieces.
When running headphones, the load impedance presented by the headphones is significantly higher than the average speaker, leading to better damping, lower power output (less taxing on the transformer) and a more present bottom end.
Both headphones and speakers will perform much better with the iron upgrade.
-PB