I stand with your hipothesis, since I'm lacking one myself. So, the game not only took (probably) a percent of my money (if not all), but also added some more. I used a trainer and finished my game with approximately 86.000.000 G when my New Game Plus started, I had :exactly 99.999.999 G.
128.69.39.118 19:22, Septem(UTC) (and how I got 21 Mr.Diggs digs in that single playthrough, I'll probably never know) My best shot of a hypothesis would be that some pseudo-consumable rewards from quests are converted into bonus money, and those consumables amounts were tampered with by trainer operation. Cheats ranged widely, from inventory 99s, to army size of six 6-members squad, skills were skyrocketing due to regular br reset and max chains.
Having finished a playthrough with cheats, I've got a new game plus with some 20+ millions at the start, I think. Is not solely number-of-completed-quests determined.