Hey -
Would be great to get an update on this, especially with regards to metaphlan4. We are seeing a similar issue when analysing the ZymoBIOMICS Microbial Community Standard that has Bacillus subtilis at a theoretical abundance of 12% (gDNA). Kraken2 gave us exactly 12% Bacillus (genus level), whereas metaphlan4 gave us Bacillus vallismortis at 0.01909%.
All the best
Tom