But then why charge for software at all if the purchase price doesn't actually reflect whatever gameplay elements the customer is paying for?

...

Or they could just do the honest thing and amortize the cost of running the servers for several years into the purchase price of the game

In an ideal world, bundling would actually be the superior method. You'll be able to see how much money you spend on server maintenance, as well as how much you spent on the actual production of the game.

Sadly, we don't live in an ideal world, so it's pretty easily abused. I'm not sure if things have changed, but Nintendo used to hold your saves hostage. You couldn't make offline backups, only online, and you can only make online backups if you pay for their service.

This was a pretty old discussion, and there was a lot of outrage back when it was announced.