They are close but not the same.
F and FA 100 f/2.8 Macro's has the same features (focus limiter). But the FA has the newer ghostless coating of the lens elements. Those has 9 elements in 8 groups and a large front lens element with 58 mm filter thread.
DFA 100 f/2.8 and the WR-version has the same lens coating, an upgraded version of the ghostless coating, and while they have a similar arrangement of 9 elements in 8 groups their optical elements differs from the F/FA, plus they have a smaller front lens element and with 49 mm filter thread.
So what does this mean optically? The two DFA versions has a higher contrast than the F and FA versions, also a more cold - or neutral - colour balance / colour rendition, where the F and FA are slightly warmer. Some has suggested that the DFA versions are actually based upon the Tokina AF 100 f/2.8 Macro, or it is the other way around. I honestly don't know.
(but the Tokina and Pentax 35 f/2.8 Macro has definately the same optics).
But I can't really say it makes so much difference on digital, the processing and auto white balance adjusts... but on analogue film, the difference in character is more noticeable, and I would rate the F and FA as being more pleasant to the eye even if the DFA versions are technically superior.