All gear has compromises including separates. I think making an assumption that separates always sound better is flawed today. When comparing separates to integrated amps today the sound quality differences will come down to design and execution, not the number of rectangular boxes. Huge power supplies with multiple chokes, big iron and coke can sized caps all in a separate chassis is no longer the only way to build a robust power supply for a preamp. Plenty of wonderful sounding tube preamps with low part counts and brilliantly designed circuits. Circuits with very short signal paths and low noise. Backert Labs comes to mind as one example.
So one can certainly find high quality preamp sections in an integrated amp. They can be found presently and one just needs to do due diligence when shopping. Also, there are some real sonic benefits to eliminating long ICs and connectors with a well designed Int amp. These shorter signal paths do have potential sonic benefits that offset some of the advantages that separates offer. Many integrated amps out there utilizing SOTA attenuation beyond an Alps pot 🙂.
Well thought out design including internal shielding and chassis vibration control can also help mitigate the advantages of separates. Simplicity does bring the opportunity for sonic gains.
Over the years I have heard integrated amps that are sonically superior to separates costing much more. I have also heard separates outperforming more  costly integrated amps. It comes down to the design implementation of the pieces in question, not simply the chassis count. Also, we listen to complete systems and the synergistic impact of the Int amp or separates also plays a role. It seems to me there are many considerations.
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