You can install Protosound 2 or 3 in some LionChief locomotives, but I can't imagine that it would be cost-effective. Lionel's "Thomas" locos specifically don't have a flywheel, so you would have to use the Electric Railroad circuit with back-EMF for motor control.
I love the idea of a custom-printed 3D superstrucutre. But I would start with a top-notch drive train, not a low-priced toy. The Williams by Bachmann 4-6-0 is a GREAT runner that will accept any electronics. But the superstructure is kind of "old timey" for me (and anyone who models the transition era.) If you could print up a huskier, more modern boiler to fit on that chassis, you would have a world-beater! Heck, I would buy one!
Personally I would buy your friend's son a LionChief PLUS or RailKing, already equipped with Proto-2 or Proto-3. These are current designs with decent performance, remote couplers and factory sound. Most LionChief Plus diesels and the PRR A5 switcher are near scale. Some RailKing diesels and their steam switchers are scale-sized too. The 0-4-0 and 0-6-0 switchers are smooth runners that run well on sharp curves. With one of these to start, he could go into hi-rail or toy trains.
Test it first yourself though, to prevent "dead on arrival" disappointments which are all too frequent. (That's one area where the crude, "zoom zoom" 1950s Lionels are better.) Kudos for trying to bring a young person into the hobby!