Currently, the RadMultiColumnComboBox has smaller height than the AutoCompleteBox or the RadComboBox for example. 

A possible workaround can be using the following styles: 

<style>
    .RadMultiColumnComboBox .k-dropdown-wrap {
        padding: 4px 12px;
    }

    .RadMultiColumnComboBox .k-select {
        width: 1.42857143em;
        height: 1.42857143em;
        position: absolute;
        box-sizing: content-box;
        top: 0;
        bottom: 0;
        right: 0;
        left: auto;
        padding: 6px;
    }
</style>