Yes they go in the [midi], like this:
[midi]
# mpu401: Type of MPU-401 to emulate.
# Possible values: intelligent, uart, none.
# mididevice: Device that will receive the MIDI data from MPU-401.
# Possible values: default, win32, alsa, oss, coreaudio, coremidi, mt32, synth, timidity, none.
# midiconfig: Special configuration options for the device driver. This is usually the id of the device you want to use.
# When using a Roland MT-32 rev. 0 as midi output device, some games may require a delay in order to prevent 'buffer overflow' issues.
# In that case, add 'delaysysex', for example: midiconfig=2 delaysysex
# See the README/Manual for more details.
# mt32reverb.mode: MT-32 reverb mode
# Possible values: 0, 1, 2, 3, auto.
# mt32reverb.time: MT-32 reverb time
# Possible values: 0, 1, 2, 3, 4, 5, 6, 7.
# mt32reverb.level: MT-32 reverb level
# Possible values: 0, 1, 2, 3, 4, 5, 6, 7.
mpu401=intelligent
mididevice=default
midiconfig=
mt32reverb.mode=auto
mt32reverb.time=5
mt32reverb.level=3