pull up a comfy chair and hang on! this site has what you need, but you have to dig for it. There is so much that could be going on. Type of guitar, type of helix/floor/stomp (that really doesn't matter), type of music, volume. Yes, you are correct that the lower volume patches will be different. Its the Fletcher Munson (spelling ?) effect. Bass and highs will get boosted more than mids when the volume is louder. (or something like that, there are very smart people on here that can help).
it could be your effects (reverbs,delays) are washing out his tone. could be he just needs to drop the gain some (you don't need as much as you think), drop the lows and highs (either on the amp and/or high/low cuts on the amp or an eq block at the end of the chain).
Jason Sadites has a ton of explanations and is very good at explaining the why of things... maybe too much sometimes, but I like it. Also John Nathan Cordy and Steve Sterlacci. all good stuff there.
Hope he sticks with it. I and others have spent many hours (mostly enjoyable) tweaking things in the helix and have gotten pretty awesome results.
Good luck