In HM12.0+Rext-4.1, a warning is sent out when transformSkipLog2MaxSize != 2.

  if (m_transformSkipLog2MaxSize!=2 && m_useTransformSkipFast)
  {
    fprintf(stderr, "***************************************************************************\n");
    fprintf(stderr, "** WARNING: Transform skip fast is enabled (which only tests NxN splits),**\n");
    fprintf(stderr, "**          but transform skip log2 max size is not 2 (4x4)              **\n");
    fprintf(stderr, "**          It may be better to disabled transform skip fast mode        **\n");
    fprintf(stderr, "***************************************************************************\n");
  }

That is, to enable transformSkip on large TU sizes, the transformSkipFast should be disabled. Otherwise, transformSkip only works when PU is NxN. However, only a warning is given. Some people may not notice this point in their simulations.

I suggest modify m_useTransformSkipFast to be false when m_transformSkipLog2MaxSize!=2. That is,

  if (m_transformSkipLog2MaxSize!=2 && m_useTransformSkipFast)
  {
    m_useTransformSkipFast = false;
    fprintf(stderr, "***************************************************************************\n");
    fprintf(stderr, "** WARNING: Transform skip fast (which only tests NxN splits) is disabled,**\n");
    fprintf(stderr, "**          when transform skip log2 max size is not 2 (4x4)              **\n");
    fprintf(stderr, "***************************************************************************\n");
  }