Some fun trivia regarding Flint in chapter 4:
If you hack your party in Mother 3 to have Flint and Lucas & Boney as per what was planned in pre-release:
• The game doesn't soft-lock, once. Putting incorrect party members in place via hacking in chapter 4 onwards tends to cause soft-locks, but Flint in chapter 4 will not cause any issues.
• As a result, even though a couple of cutscenes look a bit broken, the game will progress normally despite this. Flint will disappear after the shower discussion scene, but will reappear once you regain control. After the hot spring scene, it takes about 15 seconds or so before you regain control, but no other issues besides that.
• If Flint is on the second slot and Boney is on the third, Boney behaves normally and still says all his lines he normally does (such as before the hot spring scene), with ONE exception. Flint will say Boney's line (and stand in Boney's spot) after the DCMC finish their performance of King P's theme, and Boney reappears after the player regains control.
• Flint can equip various equipment that Lucas can also equip, including the sticks Lucas uses.
• The only unused graphic that the game calls into use if you have Flint hacked in, is of Flint dodging the train with Lucas. The game doesn't know what to do with the third party member though, and the train phases over Boney :(
• While I did mention before the game doesn't soft-lock at all, there is one optional exception that can cause a softlock. If you actually got hit by the train, the game will bug out. So… just don't get hit.
If you want more trivia regarding the battle-side of things for Flint in chapter 4, I recommend reading the pinned comment on this old video of mine. It was written by GGFan, who's someone who knows Mother 3's gameplay mechanics back to front. https://youtu.be/MCFBMSAAL7E
So, this is all to say: While the majority of any game logic and whatnot regarding Flint being in your party on chapter 4 was overwritten in the final game, there's still bits and pieces leftover, and not only that, but hacking him in still somehow works despite everything. Can't say the same thing about chapter 5 though, unfortunately.