Resolution:
This is because while deploying the engine the property which is needed is not added into the &ltdeployedengine>.tra file.
The property which you need to add in the tra file is:
"tibco.alias.&ltaliasname>=&ltpath>/&ltjarfile/zipfile>"

There are two ways you can add this:

A) You can manually add those properties in the &ltdeployedengine>.tra
file. The property which you will have to add is
tibco.alias.&ltaliasname>=&ltpath>/&ltjarfile/zipfile>
so in your case the property will look like:
tibco.alias.tibco.alias.mail=&ltpath>/mail.jar

The only issue here will be that once you undeploy/redploy  you will
have to add the properties again.

B) There is another way to add this properties as well. You can use the
bwengine.xml file which can be found under
"bw/5.2/lib/com/tibco/deployment", here you can add those property. Once
you add the property here, then you will have to build the ear again.
Now when you create a application in the Administrator, click "&ltprocess
Archive>.par" link, you will see all the properties which are added in
the .xml file. Here you can change the value to give the exact path.
Now when you deploy the engine you will see all the properties in the
&ltdeployed engine>.tra file.
Below is  format to add the property in bwengine.xml file:
&ltproperty>
       &ltname&gtAny Name you like</name>
       &ltoption&gtProperty Name used in the Alias Library</option>
       &ltdefault&gtDefault Value</default>
       &ltdescription&gtDescription of the Property</description>
    </property>

I have defined a alias library in my project. Now when I build the ear file and deploy the project , when I start the project the engine gets started but I see a error on the console which says "Error : no alias for [alias name]