According to 8.7.3.2. “Coding tree block modification process” SAO filtering should be disabled for current CU if cu_transquant_bypass_flag is equal to 1 regardless of CU encoding mode:

HEVC SCC Spec:

If one or more of the following conditions are true, saoPicture[ xSi ][ ySj ] is not modified:

1. pcm_loop_filter_disabled_flag and pcm_flag[ xYi ][ yYj ] are both equal to 1.
2. cu_transquant_bypass_flag is equal to 1.
3. SaoTypeIdx[ cIdx ][ rx ][ ry ] is equal to 0.

HM decoder (encoder) performs SAO filtering for CU encoded in palette mode even if cu_transquant_bypass_flag is equal to 1. (see function xPCMSampleRestoration which restored pixels in case of PCM or if cu_transquant_bypass_flag is equal to 1)

HM code:

Void TComSampleAdaptiveOffset::xPCMSampleRestoration (TComDataCU* pcCU, UInt uiAbsZorderIdx, UInt uiDepth, const ComponentID compID)
{

if (pcCU->getPaletteModeFlag(uiAbsZorderIdx))
{

return;

}
TComPicYuv* pcPicYuvRec = pcCU->getPic()->getPicYuvRec();