You can place a shulker box inside a shulker box using commands

Commands can bypass pretty much everything, intentionally.

For example:

/setblock ~ ~ ~ chest{Items:[{Slot:0,id:"diamond_sword",Count:127b,tag:{Enchantments:[{id:"fortune",level:127}]}}]}

Why would this be a bug?

You can also use /data merge to modify the Items inside a shulker box. I don't see how this is an issue, but confirming nevertheless.