I'm not sure what part of it they think is dangerous, perhaps I'm not reading enough into your post.

You are correct, if you build a custom gun throated for a specific type of load that may be short and jam a factory cartridge into the lands on someone, that could be dangerous. Though factory ammo is also loaded soft to add safety margin for such things.

My 300WM, even with 200gr bullets, must be loaded out well beyond SAAMI to get close enough to the lands for optimal accuracy with these bullets. Since I can do this and squeak the shells into the magazine still, I do it. My load was worked up from low charge so there is no issue. I burn a bit more powder than a SAAMI shell to get the same velocity due to the increased case capacity, but there's no problem with that for me.

My friend has a factory .308 and he cannot reach the lands with a 165gr bullet and still have it in the brass. It's still accurate, so the jump distance is not an issue in all guns.

If I were having a custom gun built, I'd have it throated for the specific bullet and load I planned to use most frequently. Since I favor long bullets it'd probably still be perfectly safe for factory loads.