The Gold Medallion upgrade only stacks once. You should only upgrade it to level 3 on one generator, leaving any other generators with it at level 0. The other upgrades do stack and should be maxed out for maximum gold bonuses. It is currently unknown whether the Rarity upgrade is additive or multiplicative when multiple generators are active.
Gold Generator - Generates 150-600 Gold Every 10 Seconds (5 Levels)
Rarity - Increases Gold Value By 1-5% (5 Levels)
Gold Medallion - Increases Amount of Time Gold Stays On The Field (3 Levels)