Drop-in replacement for Bun means that Bun supports base Node features, but it doesn't mean that it can't further expand on features. For .env Bun supports the same format as Node plus the ability to expand variables. It doesn't claim that you can replace Bun with Node; for example if you were to use Bun's own API.
Why does it really matter, Bun already supports .env files in a much better manner than Node and most of the applications developed using Nodejs will still be using dotenv package for years, I doubt if it really breaks Bun?
I dont know if this is a problem, whenever I am trying to create a project using bun i will usually find a lot of stuff which the bun either doesnot support or you have to do annoying things like playing with the commands to make it work. My favourite example is that of shadcn with bun.
Tbh, I didn't like the logic behind Bun's env expansion. And even if they want to support expansion, they should introduce a more robust system as $ is pretty common to include inside the values of an .env file
