Hey, thanks so much for the high praise!
Yeah the off-centring thing is because this is my first html5 port and I only tested fullscreen in gx.wasm and windows; now I know for next time!
I used Gamemaker engine because that's what I'm used to, but the faux 3d stuff can be done in any engine. I made a tutorial last year on the Gamemaker subreddit, because I also wrote a isometric game last year for the GMTK game jam (it's also a bit closer scale to Into The Breach). But with more experience I don't think the methods I used in that tutorial are very good (This game would run at like 1fps if I used the same method from my tutorial); the maths and basic concept is still alright though, it's just that the implementation details are very questionable.
The route we used in this game was to just draw every chunk from the back to the front, adjusting their x and y position on the screen using their virtual x, y, & z positions (their real in-game coordinates) using some maths. Before the draw step, we just added every entity to a priority queue that each chunk owned with their priority based on how close to the camera they were, during the draw step for every chunk, we just draw the entities in that chunk based on their priority. Here's a pastebin link for the draw stuff in GML (beware, it's very messy because it was obviously written in a short amount of time for the game jam).
This is not a good long term solution if you're making a non-jam game, because it meant that we had to draw the rooms and then manually set define where the ground, water, and walls are in code. Rats also have small clipping errors when they're at the borders of chunks because of this. I would probably recommend (with like low-middle level confidence/conviction) making your game with a real, 3d, orthographic camera (with a fixed 45° pitch & yaw) and then bill-board the sprites in that 3d space if you're planning on doing a long-term project. I just wrote it this way because real 3d would have taken too long to set up in the short-term in Gamemaker.