For issue #1, you could use the OnCheckBoxClick client side event handler, this event will be raise for each checked row. In your case, you will need to set the checked property to the old value if the row checker is disabled. Here is the snippet:

function wgTest_OnCheckBoxClick(controlId, tblName, colName, checkboxValue, originalCheckBoxValue)
{
	var wgTest = ISGetObject(controlId);

	var chkBoxElem = wgTest.LastChkBox;

	if (chkBoxElem.getAttribute("disabled") == true)
	    chkBoxElem.checked = originalCheckBoxValue;
	
	return true;
}

For issue #2, in the OnAfterInitualize client side event handler, you will need to retrieve the checkbox header element and set the display style to none. Here is the snippet:

function wgTest_OnAfterInitialize(controlId)
{
	var wgTest = ISGetObject(controlId);

	var headerElem = wgTest.RootTable.GetElement(WG40.COLHEADER, WG40.HTMLDIV);

	headerElem.getElementsByTagName('input')[0].style.display = "none";
	
	return true;
}

The snippet use index 0 for the input because the checkbox is the first column in the WebGrid.

In an autoincrement key value field, you will need to handle the scenario as explained on the article "New Identity Insert" in the WebGrid documentation.

Regarding the overlapping issue, you will need to set the row style to overflow hidden. Here is the snippet:

<AlternatingRowStyle CustomRules="overflow: hidden;" />
<RowStyle CustomRules="overflow: hidden;" />

The header misalignment has been submitted as a bug report to our developer. We will inform you if there is any update for this issue.

Unfortunately, WebGrid will not use the CellStyle text align property for the new row cell style. As a workaround, you will need to use the OnRowSelect client side event handler in order to apply the text align style for the new row. Here is the snippet:

function OrderDetails_WebGrid_OnRowSelect(controlId, tblName, rowIndex, rowEl)
{
	var OrderDetails_WebGrid = ISGetObject(controlId);

	if (rowEl.getAttribute("type") == "NewRow")
	{
	    var rowObj = OrderDetails_WebGrid.GetRowByElement(rowEl);
	    var rightCell = ['Quantity_WebGridColumn', 'UnitPrice_WebGridColumn'];

	    for (var i = 0; i < rightCell.length; i++)
	    {
	        rowObj.GetCell(rightCell[i]).CellElement.style.textAlign = "right";
	    }   

	}

	return true;
}

In my test, since you are using bounded data for the checkbox column you will not need to set the IsRowChecker property.

Regarding your issue, since the checkbox is bounded to the database field, you will need to make sure that the corresponding field in the database has already reflect the checkbox value in the WebGrid. The refresh button in the WebGrid will rebound the data from the database to the WebGrid again, so the rendered value reflect the databse value.