These are realtime settings which can be altered at any time during playback in Logic. If you want to destructively fix these parameters for a MIDI file export, they have to be written into the MIDI Regions before the export. Write the settings to the Regions with the local Arrange menu function:
MIDI > Insert Instrument MIDI Settings as Events
Note that the Region parameters (Transpose, Delay etc.) also have to be written into the events by "MIDI > Region > Normalize Region Parameters.