The preview of the .avs will not reflect the correct aspect ratio. The display aspect ratio (DAR) is just passed onto the container during muxing, and it is the software player (such as Haali in MPC-HC) that will read the DAR and correct the ratio during playback.
Just make sure the DAR variables are present in whichever .avs script you pass into MeGUI. In One-Click mode with pre-rendering enabled, MeGUI automatically creates a secondary .avs script for the HFYU file, but the DAR variables are placed in the original .avs and passed automatically to the container during muxing. But if you reload the secondary .avs script (for the HFYU file, eg: for a SelectEven() 30fps encode), you will have to add in the DAR variables again.
Or, if you encode to MKV, just use MKVtoolnix to change the DAR manually in a completed MKV file.