Thanks Trent and Ben for the tips. I got this working on with your suggestions. In the end it modifies the columnModel like I wanted to be able to to hide the two columns where still auto populating them when a new record is added. See code below for reference:

<script type="text/javascript">
    /* get the participant id from the request URL: this parameter is required. */
    var participantId = LABKEY.ActionURL.getParameter('participantId');

    var _grid;

    function customizeColumnModel(colModel, index, c) {
        //Hide columns
        index.ParticipantId.hidden = true;
        index.SequenceNum.hidden = true;
        index.date.renderer = Ext.util.Format.dateRenderer('m\\/d\\/Y');
    }

    function onAddProgressNote(store, records) {
        store.suspendEvents();
        for (var i=0 ; i<records.length ; i++) {
            records[i].set('ParticipantId', participantId);
            records[i].set('SequenceNum', 101);
            records[i].set('date', new Date().format("Y/m/d") );
            records[i].set('CreatedBy/Email', LABKEY.Security.currentUser.email);
        }
        store.resumeEvents();
    }

    //Use the Ext.onReady() function to define what code should
    //be executed once the page is fully loaded.
    //you must use this if you supply a renderTo config property
    Ext.onReady(function(){
        _grid = new LABKEY.ext.EditorGridPanel({
            store: new LABKEY.ext.Store({
                schemaName: 'study',
                queryName: 'progress_notes',
                columns: 'ParticipantId,SequenceNum,date,CreatedBy/Email,noteType,notes',
                filterArray: [    LABKEY.Filter.create('ParticipantId', participantId) ],
                sort: '-date',
                listeners: {
                  add: onAddProgressNote
                }
            }),
            renderTo: 'grid',
            listeners: {
              columnmodelcustomize: customizeColumnModel
            },
            width: 1000,
            autoHeight: false,
            height: 300,
            title: 'Progress Notes',
            editable: true,
            autoSave: false,
            enableFilters: true,
            enableColumnHide: false,
            firstEditableColumn: 5 //Start editing on the noteType column
        });
    });
</script>

Thanks so much!