ToME: the Tales of Maj'Eyal

This is going to sound kind of out there, but what if you could import older games you played into your current one?

So you would see your old heroes walking around the map as they did in their gameplay, and it would leave a tombstone when they die with an epitaph of their level and name and so forth.

You can't interact with these characters in any way. It might be neat to see them walking around and be reminded of what earlier playthroughs were like though.

IMO following the lore should result at least antimagic characters be hostile to magic, so that would lead to even further overpowered overworld patrols

This wouldn't really make sense, because each character goes through the same progression. For example, how is Bill the Stone Troll still alive if your previous character killed him and that character shows up in your game? Each character is like an alternate timeline.

The "bones file" idea makes more sense in games like NetHack, where you don't have lots of pre-made quests and NPCs. If you encounter your old character's grave in that game, it fits the theme of random adventurers going into a dungeon and dying. You don't have to retcon the existence of that character alongside your current one. ToME is more of a story-driven game and it doesn't work as well there.

TBH I don't feel like the world is empty. There are plenty of characters, zones, and events. You don't have tons of named NPCs walking around, but I don't feel like that's a necessity for what's essentially a dungeon-crawler.