I ran into an issue between Blueprint Shotgun and Beacon Tiles, where when mining the tiles with the gun, the beacon entities were left behind, un-mineable by hand. Presumably, this is an issue with all multi-entity buildings.

That seems like it's an issue with just tiles specifically, I made sure to raise script build/mine/revive events for entities. I'll have a look at it later and see if there's anything I can do, otherwise Beacon Tiles might need a remote interface.

I've run into this same bug.

I believe it can be fixed by changing lines 52 and 56 in tiles.lua to use params.character.mine_tile(...) instead of proxy.mine(...). It seems that mining the tile directly also removes the proxy, while firing the expected events.

Unless I'm mistaken, that changes the behavior to instantly putting the tile's mining results directly in the player's inventory, instead of the temporary script inventory. Then it would be much harder to retrieve the items mined out of the player inventory and into the script inventory where it belongs.

You're probably right about that. Unfortunately tiles just don't get the same support that entities do in the modding API :/

It would be a significant rework, but perhaps if the shotgun fired invisible single-use construction bots to do the building and mining, it would make compatibility with everything a lot easier, while also keeping the funky travel time.

I wanted to avoid using construction bots since they're pretty difficult to manage, if at all possible, and also because script rendering gives a lot more flexibility on the item rendering and such.
I've been meaning to revisit this issue as well, maybe mining the tile into a temporary character inventory instead of a player inventory (which I have infrastructure for already because of how upgrading works), or maybe a remote interface as I originally thought, we'll see.