Ok, every time they refer to "coins" in this article they really mean wallet addresses right? Is this a common way to refer to them now? It really took away from the point of the article for me.
A single address can be the recipient of multiple payments (outputs) and a transaction spends those outputs. Since each output must be referenced in a transaction, each output takes up some space and fees are calculated based on the size of the transaction in bytes, not its value in BTC. This diagram I made a few years ago might help visualise: https://github.com/olalonde/bitcoin-notes/blob/master/svg/tr...
I knew the scaling problem was bad, but I didn't realize it gets worse as Bitcoin ages!
In general, expect transactions to have two outputs. The payment, and the extra. And since outputs become inputs, transactions will average about two inputs too.
A few shavings might get orphaned here or there, but that doesn't have a huge effect on the operation of the rest of the coins.