Let template.html contain this content:
DT.SCRIPT.URL: #DT.SCRIPT.URL#
DT.SCRIPT.CODE: #DT.SCRIPT.CODE#
DT.EMBED.CODE.ONLOAD: #DT.EMBED.CODE.ONLOAD#
DT.LAUNCH.CODE: #DT.LAUNCH.CODE#

And template2.html contain this:
DT.SCRIPT.URL: #DT.SCRIPT.URL(fixedID)#
DT.SCRIPT.CODE: #DT.SCRIPT.CODE(fixedID)#
DT.EMBED.CODE.ONLOAD: #DT.EMBED.CODE.ONLOAD(fixedID)#
DT.LAUNCH.CODE: #DT.LAUNCH.CODE(fixedID)#

When I'm trying just to deploy with template I get this result:
dmitry.ginzburg@oracle-ginzburg:/local/work/packagerTestsSuite/apps/HelloWorld$ javafxpackager -deploy -v -width 100 -height 100 -outdir dist -outfile HelloWorld -name HelloWorld -appclass helloworld.HelloWorld -srcfiles dist/HelloWorld.jar -title HelloWorld -vendor Name_Surname -templateInFilename template.html -templateOutFilename dist/result.html
dmitry.ginzburg@oracle-ginzburg:/local/work/packagerTestsSuite/apps/HelloWorld$ cat dist/result.html
DT.SCRIPT.URL: http://java.com/js/dtjava.js
DT.SCRIPT.CODE: <SCRIPT src="http://java.com/js/dtjava.js"></SCRIPT>
DT.EMBED.CODE.ONLOAD: <big correct content>
DT.LAUNCH.CODE: <big correct content>

Let's try to do this with second template file: template2.html with templateId mentioned:
dmitry.ginzburg@oracle-ginzburg:/local/work/packagerTestsSuite/apps/HelloWorld$ javafxpackager -deploy -v -width 100 -height 100 -outdir dist -outfile HelloWorld -name HelloWorld -appclass helloworld.HelloWorld -srcfiles dist/HelloWorld.jar -title HelloWorld -vendor Name_Surname -templateInFilename template2.html -templateOutFilename dist/result.html -templateId fixedID
dmitry.ginzburg@oracle-ginzburg:/local/work/packagerTestsSuite/apps/HelloWorld$ cat dist/result.html
DT.SCRIPT.URL: #DT.SCRIPT.URL(fixedID)#
DT.SCRIPT.CODE: #DT.SCRIPT.CODE(fixedID)#
DT.EMBED.CODE.ONLOAD: #DT.EMBED.CODE.ONLOAD(fixedID)#
DT.LAUNCH.CODE: #DT.LAUNCH.CODE(fixedID)#

Not we can see this option (-templateId) doesn't work at all

Attaching some HelloWorld project: firstly you'll need to jar it by: ant -f simple-build.xml jar