Easy solution is to increase the variable 'buffer' size in getTileExtents.m, allowing tiles to use more of the region outside the final tile extent (create and use more 1x1km "subtile" tiles for each tile built). That would allow more overlapping area between tiles to be used for the mosaicSubTiles.m bundle adjustment step, and should improve DEM surface coherence at tile borders.
But with just the easy solution, you increase processing time, increase number of subtile files per tile, and the bundle adjustment step requires more memory(?). All while producing a lot more duplicate (redundant) subtiles between adjacent tiles.
Consider implementing a smarter method to share the created 1x1km subtiles between neighboring tiles while processing adjacent quadtiles.