If you want to use the same amp channel in more than one scene, you can. Say you have a preset wit scenes for Intro, Verse, Chorus, Bridge, amd Solo. You can have your perfect Fender clean for all but the Solo, and switch amp block channels to your Mesa MkIV for the solo. Works the same way for all blocks. A scene mostly remembers on/off state and channel selection for the blocks in your preset. There are a few other things it can do, too, but those are the meat and potatoes of it.
You can set up a channel switch to change amp channel while in the same scene, but be aware that its initial state is stored in the scene.
I know all of this, but it's still assuming that the amp channel MUST change when I go to a new scene - and that is not what I want it to do.
If I had to program each patch for each song individually, I could never get it all done. I play a lot of one-off concerts and short-run theater gigs where I have to get to a wide range of sounds, and often don't have the time to set up custom programs for each show. I might be able to pull this off for my primary band's list, but not for the other two groups that I sit in with occasionally. Thus, I have a library of stock FX patches that can mix and match with various amp settings to get what I need on the fly.
I view my sounds as a grid, with the amp channel as on dimension and the FX patches as the other. My amp has 6 gain levels accessible via footswitch. With a separate MIDI switch, I can select FX patches in groups of 10. The amp gain and FX are completely distinct, so I have instant access to 60 different possibilities, 180 if I go up or down one bank on the FX board. Forcing the amp channel to be part of the FX patch (scene) is extremely limiting in comparison - it means that I only have 8 real possibilities, and I can't change FX while leaving the amp where it is.
Now, if I could select the amp block channel separately and lock it down from scene changes, I would have a 4x8 grid of options. That's still not as flexible as 6x10, but I could make it work.
A "perfect" setup for me would be a FC-6 that could select amp block and channel, and a FC-12 that selected all of the FX, and NOT the amp block and channel. Can that be done?
FWIW, I tried one of the other high-end digital rigs for a run of shows, and this lack of flexibility was why I elected to stick with my Bogner.