Taking away the flexibility factor of separates, is my line of thinking correct?No. If you want to build an integrated amplifier that has the same performance as separates, you would have to have individual power transformers for each power amp in the box as well as whatever preamp is in the box. In a nutshell you're not likely to see that. Keeping all the ground currents straight is another engineering nightmare that has to be solved too; with individual boxes that's a lot easier!
There is also the issue of speaker cables. If you are running low impedance speakers, the cables become pretty critical and length matters! So you wind up being limited as to how far apart you can place the speakers. I like an expansive soundstage so the speakers need to be far apart; pretty tricky with everything in one box unless you have 16 ohm speakers (where the cables make less difference).
They are a compromise, plain and simple. The only reason this is a topic is because there are good integrated amps and fair separates so there is some crossover. But the best separates are not bettered by an integrated amp.