And the significance of that could get much higher with increasing value. Maybe even to the last coinbase reward being claimed.
Agree with the first sentence, but not as far as the last coinbase reward. For the last 10 halvings (or ~40 years), the block subsidy will be under 1000 sats. For 1000 sats to even be worth $100, then a single bitcoin would have to be worth $10 million. The coinbase reward will be irrelevant in the grander scheme of things long before the last coinbase reward.
So, in the future people will conduct most, if not all, of their transactions outside the base layer (the Bitcoin blockchain), which naturally will result in such undesirable outcomes as a decrease in security, privacy, censorship-resistance, and decentralization.
Not necessarily. Lightning is currently both more private and more censorship resistant (against the likes of centralized exchanges and wallets enforcing taint and blacklists) than the base layer.
The Bitcoin network will remain robust and decentralized and will be used for settlements of large transactions, but these transactions will no longer be a representation of individuals exchanging with other individuals.
Which is fine. If I'm paying for a coffee, there is no need for me to use the base layer, and Lightning brings advantages in terms of both speed and fees.