The two pixel overlap in mtm2 has caused me a few headaches that I have only recently learned how to remedy. Some of the original addon textures I made really struggle to match up with the original textures because I did not understand what the heck was going on. Now I'm still not sure I know what the heck is going on, but I know how to work around the overlap.
There are probably a lot of techniques for working with the overlap, depending on what tools you have available, so I will try to keep the definition of what is happening generic, then show you my technique with photoshop.
Basically, two pixels off of the edge of every 64x64 tile get overlapped or 'rolled under' the texture edges, you typically won't see them, so the effective 'viewing area' of your tile is only 60x60 (two pixels off each edge). Since the focus in the game blurs out the pixels a bit, it is really very forgiving of slight misalignments of this size. But, if you are using some very sharp, very straight, narrow lines, it becomes noticeable if the alignment isn't just right.
The best way to avoid this of course, is to let Traxx 1.4 do all the work for you. You can just copy your whole picture from your paint program straight into Traxx and it will cut up the group of tiles, name them, order them, and save the raw and act files. But sometimes you just want to tweak one or two tiles, so handling them manually might be the way to go.
A simple illustration of the effect is to draw a circle in your paint program in a 192x192 pixel picture. Now display your grid at 64x64 settings. Cut and paste each 64x64 texture, saving as raw/act files so you can put them into traxx. Reassemble the squares in traxx and....AARRGGGHH.
Now for the way to avoid this,
Go back to your paint program, to the original 192x192 picture. Set your grid to 60x60. Now select your first 64x64 pixel texture from the upper left, the selection area should be overlapping the grid on the right and bottom by 4 pixels. Copy and save this one with the 00 extension to the texture name. Then move the selection tool over to right and line up the top left to the second grid, again the selection area should overlap the bottom right of the grid by 4 pixels. Repeat this 7 more times for the whole picture. Reassemble the square in traxx and..... voila.
What this technique does, is keep using the top left for an anchor so that everything to the bottom right of the first texture lines up great; however, the outside edges of the whole picture are not compensated for the overlap, so those textures should include edges that are going to blend in fairly well with the surrounding ones - the generic grass and dirt textures are very forgiving for alignment overlapping.