Car "Keyless-Go" aka RKE - How it Works and Why it's Flawed by Design

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The BMW E46 LCI has a really attractively small keyfob with a built in supercap that´s charged while driving by the NFC coils. It´s watertight and didn't need any care in over 20 years of usage.

Okay, it didn't feature keyless entry and keyless go - but it was safe and sustainable. Then car manufacturers decided that their customers want big super chunky and obviously unsafe keys that need a new battery each few years. 

Not really.
supercap works if you only have an RKE key (no passive features). but then you're getting what - 15ish years of life time on average, after which you have to throw away the key (I know yours was 20years, but the average is at best 15).
Meanwhile on the same RKE keys with a CR2032, you replace a battery every 5-7 years, and keep on chugging.
Most also provide nice water tightness (there is an actual test done on them called washing machine test, and it is what it sounds like).
Sounds more sustainable to me.

With LF comm (passive features) imagine how frustrated you would be not being able to use your only-supercap key every third time due to the cap being depleted. 

Some fobs today do have supercaps, but only to support power spikes on Tx and assist the humble CR2032.

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The BMW E46 LCI has a really attractively small keyfob with a built in supercap that´s charged while driving by the NFC coils. It´s watertight and didn't need any care in over 20 years of usage.

Okay, it didn't feature keyless entry and keyless go - but it was safe and sustainable. Then car manufacturers decided that their customers want big super chunky and obviously unsafe keys that need a new battery each few years. 

Not really.
supercap works if you only have an RKE key (no passive features). but then you're getting what - 15ish years of life time on average, after which you have to throw away the key (I know yours was 20years, but the average is at best 15).
Meanwhile on the same RKE keys with a CR2032, you replace a battery every 5-7 years, and keep on chugging.
Most also provide nice water tightness (there is an actual test done on them called washing machine test, and it is what it sounds like).
Sounds more sustainable to me.

With LF comm (passive features) imagine how frustrated you would be not being able to use your only-supercap key every third time due to the cap being depleted. 

Some fobs today do have supercaps, but only to support power spikes on Tx and assist the humble CR2032.

The big advantage of the supercap approach is you can seal the key to the point where you can drive to the beach and swim with the key. Some cars, like Volvos, come with 2 large keys with buttons and a replaceable CR2032, and a smaller sealed "lifestyle" key you can take swimming. The lifestyle key's battery runs out after 2 years, and goes in the waste bin. Getting a replacement is expensive.

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The big advantage of the supercap approach is you can seal the key to the point where you can drive to the beach and swim with the key. Some cars, like Volvos, come with 2 large keys with buttons and a replaceable CR2032, and a smaller sealed "lifestyle" key you can take swimming. The lifestyle key's battery runs out after 2 years, and goes in the waste bin. Getting a replacement is expensive.

First - those accessory like passive fobs (Volvo tag, Maserati or Jaguar wearable…) are awful solutions, since as you said after 2 years they end up in the bin.
But the supercap is not the solution.
Quiescent current with passive fobs in combination with the leakage current of the super cap mean that the cap can be depleted in just several days. With the BMW RKE fob mentioned, on each startup you end up recharging it. With passive fobs you would not have that, and basically you end up using it as an NFC tag way too often.

You can have battery replaceable fobs that are watertight, it is being made, and so are such phones.
But best solution for such occasions (swimming) is probably just a passive solution like NFC (transponder pill)