Resolution:
There is a known issue for which the property java.property.automatic_mapper_if_surround=true was introduced.
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The "Mapping wizard" was creating empty tags for each optional element even if the optional elements did not appear in the input data. To avoid the empty tags in the output when the input did not contain the optional element, the user had to manually create "xsl:if" statement.  

#Set this property to 'True' in designer.tra to surround all new
optional-to-optional mappings (including child elements) by an xsl:if statement. If the system property is false or not present, child elements will not be surrounded with the xsl:if statement.
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Please add the following property in your designer.tra

java.property.automatic_mapper_if_surround=true

Please restart the designer and redo the mapping.

Before adding the property if you rt.click the root element and copy the xsl in text editor, you will see the "xsl:if" statements are missing.
After adding the above property, you will see the optional elements surrounded by xsl:if statements