Long only - Opportunity sets are limited. He can use only his +ve insight about any stock. He is constraint again shorting the stock so can not capture alpha for stock which he feels may be overvalued. Since he is not allowed to go short also limits his ability to capture +ve insights. Partial relaxation of long-only is called short extension .
Stock Based enhanced indexing - Here manager can take more independent decisions relative to derivatives based enhanced indexing strategy. IR (information ratio) is greater than derivatives based enhanced indexing for a given information coefficient (IC).
Difference between the two: I guess, enhanced indexing try to enhance return in a risk controlled manner. Manager uses strategy to replicate the benchmark & generate return to make for the administrative , transaction cost. As CP mentioned, Stock based enhanced indexing will have a lower tracking error than long only.