Another problem that would arise if bitcoin becomes so valuable that one satoshi is one USD is that transaction costs would make it impossible to spend the bitcoins. Right now, even a one satoshi transaction would require a few hundreds or thousand satoshi in transaction fees.
This is much less of an issue. Although a satoshi is the base unit in the protocol (meaning introducing smaller units would require a hard fork), this is not the case for fees. Although we all think in terms of sats/vbyte for fees, in the protocol fees are actually define in terms of sats per virtual kilobyte, or kvb. The default setting is 1000 sats/kvb, which is obviously the same as 1 sat/vbyte. Because of this, if is easy to change that to 100 sats/kvb (for example), which would be the same as 0.1 sats/vbyte (which would obviously then be rounded up to the nearest sat). Indeed, not only do we not need to fork for this, but we don't even need an update to Core at all. Any node is free to change their minimum fee rate at any time, and miners are free to include any transaction paying any fee they like at any time.
Is it possible to create a second layer on top of Bitcoin or a third layer on top of the second to allow payments under 1 satoshi and only return to layer 2 or 1 if you own exact amounts of Satoshi's with no decimals?
You can already do this with Lightning. You can open a channel and make transactions involving millisats for as long as your channel remains open. If you try to close a channel which is holding some fraction of a satoshi, then the balance you receive will be floored to the nearest satoshi.
So for example I open a channel with 100,000,000 msats. I transact back and forth over several months. At the end of those months my channel has 100,045,724 msats. If I close the channel, I'll receive 100,045 sats.