I did some testing and comparison with the various files created by the manual FSET and automatic AeroScenery processes and after a few false starts I think I have an answer.
I used the same FS2 level 13 grid in FSET and Aeroscenery and set about to produce the output, then compared the results. Both TMCs were run through Geoconvert with Mask enabled.
Output files created- FSET = 1, AeroScenery 3 =3. Note all images below show FSET on the left and AeroScenery on the right.
The extra ttc (70a0) created by AerScenery was a strip across the bottom of the tile, hence the additional mask file needed. Looking at the source stitch file, the texture is from the top of the stitch image, so it in effect fits on the top of full tile created. Look at the enlarged image below to see the strip as the thumbnail process chops it off. Running the extract with masks off would have seen the mask tiles not created. I had found in my earlier scenery creation attempts that when a source image spanned multiple grids in FS2, and you are running GeoConvert for that grid level with masks off, then Geoconvert discards those tiles that would have resulted in a partial tile (mask tile). Same thing occurs with transparencies.
TMC comparision - no difference here
AID files - difference in lat of the top left coordinate, the first clue I think.
Lastly I compared the source graphic files created from the image data that is read by GeoConvert. What I found was the AeroScenery stitch file was taller than the compiled BMP created by FSET. The AeroScenery stitch image has a horizontal strip of image at both the top and bottom compared to the FSET file. In the AeroScenery stitch image the extra strip at the bottom is roughly double the size of the extra strip at the top. In the image comparison below note the small creek at the bottom right of the AeroScenery image, and the small oval at the top. Both these are missing from the FSET extracted image. The width is the same in both.
Source image comparison - note extra height in the right image created by AeroScenery
When running GeoConvert (using an identical TMC file for both remember) the extra strip at the bottom of the AeroScenery image appears to be ignored by Geoconvert. But the extra strip at the top of the AeroScenery stitch image appears in the additional files created by the mask option. I am assuming that as the FSET source image file more closely matches the FS2 tile's width to height ratio, no mask files are created as there is no additional image area to be cut off.
Raw file comparison of the same output file produced by both processes - both are identical except for some colour variation. The top and bottom of the AeroScenery image is discarded by GeoConvert resulting in the same output image as from FSET.
So there appear to be 3 courses of action.
1. Do nothing in AeroScenery and just run with masks off. This will discard the extra portion of the taller AeroScenery image. The top section of the image used in the mask file has a distinctive oval in it, so I was able to confirm that this strip also appeared as the bottom section of the full image of the tile above when that grid was extracted. So using masks off and discarding the additional image data will not compromise the scenery output accuracy. But using masks off will cause problems where transparencies are used.
2. Do nothing in AeroScenery and run with masks on. This would mean that FS2 has 2 image tiles created for the same data for the same level. So the images in the strip across the mask tile will also appear as part of another full tile. Not sure if that has any impact, but I did read in another thread that mask file sometimes cause visual issues in FS2. Can't remember the issue though.
3. Modify AeroScenery to reduce the overscan in the stitch file. Masks can be left on to allow for transparencies and this will not impact the output file creation as it does now.
The image below shows the size and coordinates used by FSET that produced the FSET equivalent of the stitch file. Perhaps you could compare these details with that used by AeroScenery.
Just as a side point, but I had to run the FSET process a couple of times to try and get a good match of the respective output file resolution. I had to try different download sizes in FSET to match the zoom level in AeroScenery, since they describe the image quality differently. I ran 3 extracts in total at different image quality levels and in just one of those, the FSET data produced mask files. However when I looked at the mask file it was just a single line of pixels across the bottom. So FSET occasionally has some very small variations that produce mask files, but they are rare.
I have been looking at this so long my eyes are starting to bleed. Time for a break.