According to Ordnance Survey Ireland, there is no difference between EPSG:29902 and 29903, although the EPSG has a different opinion. At Safe, we try to follow the lead of the originating authority, and so both EPSG definitions map to the same FME definition, which we map to the TM75 WKT when writing to Esri formats.
When reading from Esri formats, like shape files, FME retains the original WKT, which is used when writing back to Esri formats. This is why converting from shape files produces the TM65 coordinate system for the output.
We have created a workaround for customers who would prefer the EPSG differentiation. Please copy the files in the attached zip into the following folders on your computer:
IrishNationalGrid.fme -> Documents\FME\CoordinateSystems
IrishNationalGrid.db -> Documents\FME\CoordinateSystemExceptions
After restarting FME, EPSG:29902 and 29903 will map to separate FME coordinate systems, which in turn will map to the appropriate Esri definitions.