Got it to work using the following code in /usr/share/ebox/stubs/mail/main.cf.mas just before the "</%init>" tag.
my $userMainCF;
if (open(FH, "/etc/postfix/user-main.cf")) {
$userMainCF = join('', <FH>);
close FH;
}
</%init>
and then at the end of the file:
<% $userMainCF %>