[yess]

I found a solution that works well for me.

I moved the list of files to be included to an xml file and in that one I can use the non-debug tags:

<Ui xmlns="http://www.blizzard.com/wow/ui/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.blizzard.com/wow/ui/
..\FrameXML\UI.xsd">
  <!--@non-debug@
  <Script file="LibStub\LibStub.lua" />
  <Include file="CallbackHandler-1.0\CallbackHandler-1.0.xml" />
  <Include file="AceAddon-3.0\AceAddon-3.0.xml" />
  ...
  @end-non-debug@-->
</Ui>

That way I do not get the annoying errors during development and in the released version they are included as the packer changes the tags so that the lines are not commented out.