I dug into this, but I can't find an appropriate fix in PSR. I tried to update it via tomlkit only, and it works, but tomlkit + dotty-dict seems to be the problem.

One thing to note is that this is a case of an out-of-order table, which is discouraged by the TOML spec:

Defining tables out-of-order is discouraged.

# VALID BUT DISCOURAGED
[fruit.apple]
[animal]
[fruit.orange]

# RECOMMENDED
[fruit.apple]
[fruit.orange]
[animal]

If the table is as recommended in the specs, the test passes.