Does that verson come with a factory base map that includes, down pipe, intake, intercooler?

 

The FD3S4 one you speak of, which is all but the earliest PFC's, has a less aggressive timing map than the earliest PFC's. There's really no guarantee it will work safely with that kind of setup. It might, it might not. There's no way to tell for sure without logging data.

 

Would it at least be better then the stock ECU?

 

The early PFCs has a stock map on them and the program version was
2.01B. That is the default map for the old FD3S beige datalogic software.

Then about 1999 the 7.07 map came out for improved 1999 engine.
About the same time the default PFC map was the 5.07 which was for a modded stock twins engine.

The newer PFC map is the same as the 5.07 but is labeled 5.08.