It makes sense it used the LA Remake style. It's the new design over the Overhead games. It wasn't just a remake thing. It's quite specifically the latest design. Not unlike how the Toon design inspired by the newer Overhead games at the time. It fits how this happened. Or for another example, SS is also a cartoony style. BOTW and TOTK share a very similar aesthetic. (Incidentally, if we had Oracle remakes, they'd be using that style anyway. It makes way too much sense, as they were built off of the LA engine from the start. So it continuing is good~).
In fact, the last Toon style game was ALBW too.
Besides, Zelda isn't Link. She sometimes has similarities to him, but these are unique situations; BOTW/TOTK she's not playable anyway, and she's an extremely different person. The CD-i games were meant to emulate the first two Zelda games playstyle-wise, as no other styles existed. But still did their own thing. In fact, it still had OHKO items(against some Bosses), which was not normal even then in the same way, as they are all Trade Items compared to, say, the Bow oneshotting the weaker Gohma. The last one is that she was like him in the TV Show(also where the CD-i games took inspiration from).
We also don't know where this is meant to be in the timeline. Considering everything, it can't be after TOTK, but could be in other spots. Maybe it's before ALBW. Maybe Ganon isn't entirely dead after that game either. Or maybe it's after LA as is. Hell, it could be a new part of FSA, with Ganon coming back. In fact, the Trident being so awkward in how it works would make great sense to place it after that game, since it broke conventions too with a new form of multiplayer(very different from the original FS).
As for it breaking conventions in general... I honestly would've found Zelda being essentially a skin for Link a very boring way to take the series. She already was pretty bleh in Spirit Tracks due to not truly being playable. We have tons of Randomizers, Romhacks, and other materials where she does that. Her being actually different just plain makes sense. Just like I'd expect a game starring Ganon/dorf to not be a traditional Zelda either. I'm glad they tried to change it up. I think the new mechanic is genius and really ties into how she's supposed to be the Puzzle-oriented personality. She's tactical. She's not about Courage. She's Wisdom. We just need a Power-related game down the line. How they do that, who knows.