McIntosh MC240 Question

"I'm wondering what the explanation is for the difference given that gain controls wide open or running without those controls should be the same input level."

You're amplifying the signal 2x. First in the preamp and then again when it reaches the active gain stage in your amp. I wouldn't do it that way. The system should sound much better if you just use the preamp to control the signal gain and not the one in the amp.

"I would have thought the opposite ... that increasing the gain at the power amp level would sound cleaner as opposed to increasing gain at the preamp level, which would be one level further away from the power source. In a single line source system, you could run the source directly from the power amp ... yes?"

Almost certainly, no. Think of it this way. Would you go out and buy 2 preamps? That's what's going on here. The active gain controls inside the power amp are essentially a preamp. That's why he's getting almost no volume control. He's turning the volume on the preamp inside the amp all the way up leaving almost no adjustment.

A far as using the preamp in the amp or his stand alone preamp, there's no real way to tell what one will sound better. If I had to guess, I would go with the external preamp, and bypass the one in the amp. Most likely the external preamp is a better design. Especially the volume control. The reason they put gain controls on the amp is not to bypass a preamp, but to allow better volume control in situations like multi room installs, home theatre and possibly biamping. But in a high end audio system, I can't think of a reason that you would ever want to use 2 line stages and link them together. You're putting another component in the signal chain for absolutely no reason.