I would take a safe Maildir implementation over subtle (or sometimes catastrophic) data loss bugs any day. The one really serious problem I have with Thunderbird is that after being stung more than once, I feel like not only do I have to keep normal backups, I also have to retain old backups indefinitely, just in case a folder was corrupted silently a long time ago and I only find out months or years later when I need to search older messages.

That's ~4MB per thousand emails; while I agree it's conceptually wasteful, I doubt it would have any real consequences for anyone.

Only if you use filesystem that cannot efficiently store small files, either together with metadata or packing several small files together, and allocates a full allocation unit for each separately.

Maildir, as opposed to emails stored in one big file, does cause some disk space to get wasted, but in past 10 years, it is immaterial. Even million empty emails, each taking 4kB of disk space, would take only 4GB in total. The small files aren't a concern for saving disk space: the big ones are.

Maildir has the advantage that searching, adding and deleting emails is very fast, much faster than if those operations were made on single big file. Worth it.