It sounds like you have played through the game, probably multiple times, and from that point of view, you are absolutely correct. There is no reason to wait until the end game, gain that minor pittance of cash, and 'complete' a quest just for completion sake.
Think about it from the point of someone that has never played the game before and is coming into the game in a 'fresh, blind' play through.
At that point, they would have no magic Multiverse pod to use from a previous save, no super bots earning millions of credits, and are struggling to afford BFT torpedoes or MK II ship gear. 50 million credits can be a hell of a boon IF you are someone just starting out in the game for the first time.
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That was how it was for me the very first time I played the game. Gaining 50 million credits NOW, was much more helpful than gaining 50-100 million credits over time from a sexy super bot in the arcade.
My second play through had a multiverse pod that was loaded with collapsar and voron torpedoes, highly skilled and well trained bots, MK II and MK III ship components, a Hell Hammer with 6 underverse effectors, a barbed carapace to sell for cash and a stack of cloak and engine action modules.
But for that very first play through, the 50 million credits was a much better boost (to me), mostly since I only had Gen 1 and 2 bot frames to put shells on.