so yes for fixing seams, (only for sprite tiles)
(this is from my first test, so i dont know yet what can be modified and what not)
original map i imported in c2
i added 1pixel padding around clusters (so they don't touch there borders and also not touch other clusters)
too better show the 16pixel grid and placement
import > this is in import sprite strip
notice that i only use 7*16 tiles, instead of, 8*16 tiles that would fit a 128 texture, this is because the automatic texturepacker adds a 1px transparent border around the tiles, if you use 8 it will scramble you imageclusters in different textures
(note, in this example i could have filled the 7th row with something)
after export (this is the actual map i used in tiled, again not yet totally sure if i could also use the originial
modified texture, i start at the top dragged the pixels from just above the 1px gap on top of the transparent area (you can drag a whole row over it) then did the same from left to right, (you wont notice this as instead of a transparent line it will be the same color pixel that gets blurred in)
this can be done pretty fast, the outside borders (off the full texture) i just filled in with the grass color
replace the original exported with the modified, result
https://dl.dropboxusercontent.com/u/61666915/noseamtest/index.html
so yes, its not the perfect workflow, but i hope this helps, and i hope there's a better workflow in the future