Square Enix holds their games ransom, because they know if they hold out long enough, Nintendo will bend over and do it. They've been doing that since the Wii/DS age. They dont do that SONY. All those SE games that Nintendo published, if they PS games, SE would have published them promptly.
I'm not really in the mood to argue over publishing and who does what in terms of publishing but yes compared to where Nintendo and Square were and where they are now their relationship is much better. At least Nintendo gets Square Enix games now. And when I say Square Enix I'm mostly talking about Square. Enix and Nintendo retained and still have a great relationship in terms of software releases from the NES to the Switch. The first Dragon Quest game was published by Nintendo in the US, doesn't mean that meant Nintendo and Enix were in a rocky relationship far from it. It had to do more with understanding the market.
On Nintendo Switch, the Dragon Quest 1-3 remasters, FFCC, FFVII, VIII, IX, FFX-X2HD, XII, Collection of Saga, Romancing Saga II, FFXV Pocket, World of FF Maxima etc. are all published by Square Enix.
There are reasons why I feel Nintendo chooses to publish some SE's games outside the US now. But that would only be speculation. The fact of the matter is that compared to the late 90's, things are much better and could facilitate more collaboration between Nintendo and SE. I know it's kind of wishful thinking as I feel some of SE's divisions feel they've outgrown this kind of work, but hey we can dream.