Before => reproject_before \ 
                             => merge
After => reproject_after   /

Before => before_reprojection \
                                => after_reprojection => merge
After =>                      / 

before = pdal.Reader.las("before.las")
after = pdal.Reader.las("after.las")

reproject_before = pdal.Filter.reprojection(out_srs="EPSG:26915")
reproject_after = pdal.Filter.reprojection(out_srs="EPSG:26915")

merge = ((before |reproject_before) | (after | reproject_after)) | pdal.Filter.merge()

print (merge.pipeline)

{
  "pipeline":
  [
    {
      "filename": "before.las",
      "tag": "readers_las1",
      "type": "readers.las"
    },
    {
      "inputs":
      [
        "readers_las1"
      ],
      "out_srs": "EPSG:26915",
      "tag": "filters_reprojection1",
      "type": "filters.reprojection"
    },
    {
      "filename": "after.las",
      "tag": "readers_las2",
      "type": "readers.las"
    },
    {
      "inputs":
      [
        "filters_reprojection1",
        "readers_las2"
      ],
      "out_srs": "EPSG:26915",
      "tag": "filters_reprojection2",
      "type": "filters.reprojection"
    },
    {
      "inputs":
      [
        "filters_reprojection2"
      ],
      "tag": "filters_merge1",
      "type": "filters.merge"
    }
  ]
}