I do not think you can disable the regeneration of domain.xml.
I guess the question that I would have is 'why do you want to disable or alter the doctype?'
Why do I ask? It looks like you are trying to compensate for a bug in the server or in a tool that you use to read the domain.xml file. While your solution may help you work-around the issue, no one will be able to fix the thing that you are working around without a bit more detail.
With a bit more info, we may be able to help you be successful (in the short term) and improve the quality of the software that you are using (which will have benefits for a whole bunch of people).
vbk
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