When I run notmuch I get a bunch (hundreds) of emails that are ignored
with:

Note: Ignoring non-mail file: ...

The files are valid maildir files but have a paragraph somewhere in the
body where someone has written "From ".

And do they also have have a line starting with "From " as the first
line? This makes them mbox files. The second "From " makes them mbox
files with multiple messages. Notmuch thinks your MDA (the thing that
made those files) is misconfigured, assuming my guess about the format
is correct.

Every message file begins with “From “. This is true of all messages downloaded by both offlineimap (with type = Maildir) and mbsync.
neomutt has no issues dealing with these files as maildir and mu has no issues indexing them either. I’m assuming that stating with “From “ is part of the maildir spec.

The problem occurs specifically with notmuch. If someone sends a message with a line that begins with “From “ in the body then it confuses notmuch.

mu can correctly index these messages but my mu is linked against libgmime-2.6, my notmuch (0.28.3) is linked against libgmime-3.0.

Is there a fix to force the recognition of maildir files in this case? I
thought this was a solved problem with gmime since 2.6.7.

There is not currently a way to do that. It's not a GMime problem, it's
a design choice of notmuch to avoid parsing multiple message
mbox's. That was originally added as a safety feature, and I think it
should probably stay the default. If someone wants work on adding a
configuration switch I can point them in the right direction.

This is a poor design decision. It means anyone on the internet can break your mail setup simply by sending a message with a line starting with “From “.
(and using usual quoted-printable Content-Transfer-Encoding).

Try it. Send yourself a message with the line “From bad parsing comes chaos” and see if your notmuch can find it. My version can’t.