Well, I actually love both methods almost equally, but I like the old method a little bit more:
The current method makes us able to modify the new thing to paste in a wysiwyg way easily, while the old method will force us to maybe paste the old data somewhere to modify it, then copy it again. It could be also used to create some kind of "Mirror biome" or some weird labyrinth features.
The old method is a little more complex to make it work, but it is a lot more powerful. For example, my "Fort boyard gold coins shower" requires 3 tileCopier, with the current method, plus the fact that (i guess for now?) only square and circle areas exist, it takes a lot of space, and forces me to copy and paste the shower multiple times. In some "tight" areas, you might be forced to have the copies far away from the original, making it kind of difficult to wire them, especially during nights and those *****ng blood moons.
I'm not sure but, the old method might be able to store the alternate sprite number to make those blend properly too, at the cost of 16 or 32 bits added per tile ?
(Also ... the old method could be easier to hijack to make it read data in files/url by some crazy modders that could need to modify a running server from the outside, or in the opposite side, send the world modifications of an area to an external website for some reasons [Even if it's obvious that this kind of reasons lives outside of what this mod is meant for, having the ability to stay close to its implementation and to use the same datatypes makes it way better])
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About the hitwire being unable to get called on empty coordinates, I can see two solutions, one that is a workaround that might be either totally unsafe or needing a lot of work to be safe, and one that feels both intuitive and weird for some reasons, so i'm not sure.
The workaround would be to check at pins positions if there is a tile behind, and if there is none, place an invisible ModTile at this location, i guess during both the moment where you place vanilla wires, and the moment where you place devices, but it would get messy once you start placing tiles on top of the device (i guess you'll need to delete the modtile), and when you kill tiles at this coordinates (you'll need to place back the modtile), which might be complex when tiles are bigger than 1² I guess.
The other way would be to create either a new tile, or an object copied from the actuator that would live on the same layer, and would act like a trigger device. It would stay invisible like other devices and actuators, but would require a tile to live on and would get destroyed if the tile gets killed. Placing those would require a different workflow and would look like a bit different than other devices, but I feel like it fits well as it is a vanilla to mod converter, and might even feel more natural to have to do something different to make it work than having stuffs that just magically work (On top of that, I didn't find how to make the devices appear on screen while placing vanilla wires). In my head, placing a vanilla wire on a pin feels way too weird, and might lead to people (me) placing vanilla wires on devices by mistake, thinking that it shouldn't interact one with each other.
Could the double call to HitWire be caused by the fact it somehow gets called both on the tile behind, and on the pin, while you check for every hitwire that happens at those coordinates ?