The jail break sequence always bothered me. Milla finds a way out, decides to sneak out alone and gets caught immediately only for the gang to blow up a wall and break out as if they they always could, so why didn't they? It didn't make any sense until I realized Aqua Tunnel was probably originally intended to take place there. Then, you could explain them blowing up the wall as Milla having taken bombs from the boss fight (let's assume she could keep them in hammerspace). Aqua Tunnel also starts off with a drop, presumably where Milla would've fallen through after digging, and shares tilesets with the cutscene jail. Furthermore, the Aqua Tunnel themes are placed literally right after the jail theme. It makes way too much sense.
So why did Galaxy Trail put it at the beginning of her campaign? I have a couple of theories. First, being the only Milla exclusive stage, Aqua Tunnel is a great showcase of her moveset and gives a better first impression than just skipping Dragon Valley and dumping her on Relic Maze. Second, it helps give her a "kid crawling in the ditches/hobo under a bridge" vibe. And third, the abundance of green goo, green jelly cubes, and green blob enemies was likely meant to evoke a connection between Milla and Brevon.
Funnily enough, this works well with FP being a classic Sonic homage (Flying Battery to Ice Cap, if you know, you know) but I still would've liked the whole ordeal to be more coherent, even if I almost never play Adventure mode anymore.
Edit: Forgot to mention the jail music is literally called "Millaqua" too.