Doesn't check all the boxes, but Metal Gear Solid 3: Snake Eater hits a lot of notes, most notably in the boss fight department.
3rd person, Cold War spy, stealth, action game
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A hunger mechanic that effected performance (stamina and at around 50% would affect aim or have stomach growls that would alert enemies) and could get food via hunting, trapping or stealing and in a few situations could be used offensively
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Camo system
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Majority of the bosses that you could defeat lethally or no lethally
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Medical system was pretty nifty, not fully realistic doing first aid during battle, but had the spirit of battle injury management
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Can get a lot of lore tidbits here and there by being stealthy and eavesdropping either being nearby or using a longe range listening device and by communicating with your operational support
And there is probably other systems I am forgetting ( played it on a ps2 many moons ago). Seems there is a pc version but appears to be a port and with a controller requirement, but otherwise I thought it was a loaded game for its time ( released 2004)