Women with high FSH tend to recruit follies early, thus leading to high E2 on days 2-3 (E2 is released from those early follies). This is why women with high FSh tend to have shorter cycles (they ovulate early). This sends FSH down, giving the women a false low FSH reading.
This is why EPP often works well with women with high FSH, it keeps FSH down early and allows the recruitment of more folies.
Low E2 is not usually as big a problem, but I think is also a sign of decreased reserve. I'm surprised he wouldn't take FSH as a true reading there, my doctors always did.
Hope this helps, I actually tended to have low E2 readings on day 2/3, and EPP helped with that.