Elder Scrolls Online is probably the best modern example, although there have been others over the years. Even so, I think most of those examples did not allow cross-platform play, so the concept of needing to buy multiple licenses in order to play the same character across multiple platforms doesn't even exist in those cases.
That said... Square Enix definitely has a reputation for its arcane (complicated) account and billing practices, at least among their North American audience. When someone makes a statement that SE account management "seems needlessly complex" it's certainly true. Just as a recent example, I pre-ordered Stormblood and normally I would expect to just log into my account in the store and the purchase with all perks would automatically apply itself to my account like you would normally expect with any other game. Instead, after making the purchase from one website, I had to log into another website to apply the purchase to my account, and then had to log into another website in order to apply the promo code for the item bonuses to my account. The fact that all three websites use the same log-in credentials makes this seem super unnecessary and complicated. And I'm fortunate enough to have only ever played on a single platform for FFXIV using a single account that goes all the way back to early FFXI days, so it's relatively simple for me most of the time. I always sympathize with anyone who has a question about billing or accounts, especially when it involves multiple licences, because it's almost never an obvious answer to find so no wonder they had a question about it.
If I had to guess why they do it the way they do... I'd guess that their account/billing choices are more consistent with typical Japanese and/or Asian practices rather than the western ones that we are used to, so some of the ways they organize their sites and rules just feels weird to us but might be perfectly normal to someone from Japan. Just a guess, mind you. I know that when I find myself on a website that is clearly intended for a Japanese audience - for example, a popular fansite or a Japanese tv show's website - the typical layout, linking structure, and overall navigation is often very different from what I would normally expect of a similar type of page intended for a North American audience. But that's purely anecdotal and subjective observation, so take it as you will.