Not sure how you could do this with FME Desktop alone, but if you have access to ArcGIS Pro or another GIS program you could digitize the area of each raster that you want to keep and then clip the raster based on those polygons. It would take a lot of manual work but you'd be able to control exactly the extent of each raster will end up in the final result when they're all stitched together.

Hi @louis_boekhoudt​ it should be possible to remove borders from rasters using FME! A combination of clipping the borders and setting the outside area to be transparent should do the trick.

@mark2atsafe​ wrote a great article here outlining these steps. Additionally, @Takashi Iijima​ also provided a great solution here. If neither of these solutions work for your imagery, you could also try looking at the RasterSubsetter transformer. It's a bit less intuitive, but if you know the extents of the borders in your imagery are all the same then this could be a useful approach.

Hope this helps out!