Here is how I imagine the workflow with the Mixpre-6, based on these recent clarifications:
In Basic Mode, the unit operates like a true field mixer. The user, with headphone monitoring, can make a live matrix mix on the fly down to a 2 track stereo recording. The channel knobs control the gain for each channel, but the only thing recorded is the final stereo mix. If only one pair of mics or one pair of line input tracks are being recorded, then the unit works basically like any other stereo recorder. The control knobs work just like we are used to with other recorders, and there is the option to control gain by individual channel, or by linking them to one knob for gain, with the one next to it serving as a L/R pan control knob.
In Advanced or Custom mode, the knobs still work as they do in Basic Mode, controlling each channel in relation to a mix down to stereo tracks. The difference here is that in addition to the mixing mode, the ISO tracks can be recorded separately, so a post mix version can be put together afterwards. Since these tracks are recorded "pre fader", it allows the user to play around with a live mix on the fly, while still having the individual tracks captured without being impacted by the user riding the faders for the stereo live mix.
Gain for each channel can be adjusted separately, by pushing each channel knob individually to adjust the gain for one specific channel at a time. The limitation here is that you can't see on the display the relationships between tracks with all tracks peak levels displayed on the touchscreen at the same time. This is a clear departure in workflow from a 744T or an R44, where all the tracks are shown on the display and you can adjust one track while seeing a meter display of all the tracks at the same time. This situation explains the reason for the paragraph on page 20 of the user guide "A Little Bit About Gain". In a nutshell, the message calls for a change in thinking about the relationship of gain and how it impacts the final result. Trying to record an ideal level that is maximized to be as close to 0db on the meters as possible, something we all worked towards with 16bit recording in the past, is not necessary.
Sound Devices is proposing that since the preamps have such a huge range between the noise floor and the maximum input level, it's a waste of time trying to record the ISO tracks with perfect levels. Even if the ISO tracks are all recorded with maximum peaks only hitting -12 or -6 on the meters, there will be no issue with bumping the gain in post to -1 or 0 if desired. A practical example would go like this: Assume you are interested in recording a simple matrix, blending 2 mic channels with 2 soundboard channels. You can play around with delay on the mics to account for the distance from the stage, and use headphones to mix the 4 channels together and that mix will be recorded on the dedicated stereo tracks. Meanwhile, since headphones can be very misleading in a loud concert environment, the individual ISO tracks set to a moderate level with max peaks at -6db on the meters will serve as a backup, offering a second chance to create a mix later in post.
So, it's not perfect by any means, but when I think about it my initial skepticism I realize that it may be based on a perceived need that really doesn't exist anymore. In fact, it could be viewed as a benefit. With this unit you can be all over the map with the level adjustments for the live mix without worry, because if you screw up you still have an unaltered version of the ISO tracks preserved to try it again later in post. And, if you need to add gain to any of those tracks to lift them up in volume, they claim the difference between the tracks with bumped up levels in post vs. levels captured at the "ideal" maximized word length to begin with is no longer an issue worth worrying about.
I'm still not convinced this unit is what I would want for a multitrack recorder at the sub-$1k price point, but the ISO gain workflow is not a show stopper by any means. I'm still holding out hope that Marantz Pro will introduce that PMD-706. From looking closely at the banner for that 6 channel unit that was briefly shown on their website, I'm expecting the form factor to be more like the rest of the current lineup from Marantz, with the case being deeper than it is wide, similar to the Zoom H6 layout.