Are there any negatives in using atomic swaps? It seems like the best possible solution(?). I cannot see any negatives and it does seem like it offers close to 100% privacy.
There's indeed still an issue I forgot to mention and you already suspected: In all solutions where you exchange a Bitcoin UTXO for another one coming originally from another person, e.g. CoinJoins and also atomic swaps, you could actually end up with coins from a doubtful source.
If your route is BTC -> XMR -> BTC then the obvious problematic step is the XMR -> BTC part. If you already did some transactions with XMR to obfuscate the amount, maybe for this step it is actually advisable to use a trustable non-KYC exchange (see link in my first post for several options). Or, if you know how to do it, check the Bitcoin UTXO's provenance (but be careful to not expose your privacy in this step, as chain analysis tools can check the IP addresses from those querying an UTXO ...).
Another possible negative for atomic swaps is that it can be difficult to find an exchange partner.
https://kycnot.me has some platforms for atomic swaps too.
I know that coinjoin was very popular before but now it is known that it can be easily flagged. Maybe it is harder to prove source of funds?
In CoinJoins it is easy to prove source of funds: simply prove you own all addresses involved (sender and those recipients who receive your coins).
In atomic swaps you should always be able to prove the source of funds as long as you keep stored all data involved, i.e. all addresses, private/public keys, amounts and transactions IDs, however I don't know the exact procedure in the case of atomic swaps with adaptor signatures. You can easily prove that you sent an amount and received an amount on the target blockchain. But I don't know how you do the "connection" here, apart from the amount itself (which can be variable due to the exchange rate).
Is there a risk of ending up with tainted coins when you move back to the blockchain after using the lightning network?