As I understand it, you have some inquiries related to the matlab model for FFT. Just would like to check with you on the following:
1. Which device and Quartus version are you using?
2. Where is the specific location of the matlab file that you are looking at?
3. Probably you can share you FFT IP file so that I can have better understanding on your configuration.
By the way, based on my previous experience, generally we will configure the FFT IP, then click on Generate Example Design button and we will find the right model under *_example_design/Matlab_model. Not sure if you are using this method to generate the Matlab model.
Please let me know if there is any concern. Thank you.