You ask for thoughts, so here are two. Usual disclaimer: I am an amateur (i.e. railfan), not an industry insider or an engineer, so take my thoughts with appropriate amounts of salt.
(1) The GEVO engine has been used in passenger units: the ones built (by??? but surely with advice from GE, who provided the innards) for the Boston transit agency. Looking at how they are working out would give good indication of what a GEVO-powered successor to the Genesis could do (at least in non-high speed service).
(2) Weight. The GEVO-12 is a very heavy engine. (The HDL engine, of less than blessed memory, was already heavy. Part of what went into the original GEVO was a lot of cast iron to stiffen the frame to eliminate vibration problems experienced with the HDL. The current, Tier 4, GEVO is probably even heavier.). Now, weight is a BAD thing in a high-speed passenger locomotive: it's not needed for adhesion at high speeds, and it increases the damage to track from "hammer blow." American passenger diesels of the past few decades are already heavy: heavy enough that I have a couple of times speculated about reviving the A1A truck to spread their 280,000+ pounds over more wheels(*). The "Charger" is intended for fast service: I think it is designed to allow 125mph. So there would be an incentive to do whatever one could to reduce the weight. And the Cummins engine... I don't know how much it weighs, but it is smaller in cylinder (and so, one would presume, over-all) dimensions than the GEVO or even the FDL: so, at a guess, the 16-cylinder Cummins engine used in the "Charger" is lighter in weight than the GEVO-12. ... GE had (I don't know whether this was included in the spin-off of the locomotive-building division) a smaller, lighter, engine, which was used in a number (fairly small number so far) of units for Britain (where permissible axle loadings are such that British six-axle units weigh about as much as heavy American four-axle) and for narrow-gauge service in Queensland (Australia): the "Powerline" engine. I have wondered whether a GE passenger locomotive might have used this engine (which, of course, would have been just as untried as the Cummins engine in mainline U.S. service).
(*) Fantasy: mount something like a Genesis, or a GEVO-version thereof, on six-wheel trucks. It would probably end up longer than the Genesis we know and love to accommodate the longer-wheelbase trucks. The works would not need the extra length, so part of it could go into the nose. At which point, I think, it would be feasible to do the sheet-metal-work in a way that would make it a lookalike of an earlier GE passenger unit: the Alco-GE PA-1 (whose carbody was designed, not by Alco, but by a GE industrial designer). This would surely convince more rail fans to ride Amtrak!