Since no one answered me I will post what I used as a solution to this problem in case someone else has a similar issue.
I ended up creating my own version of these template files:
PojoConstructors.ftl, PojoFields.ftl and PojoPropertyAccessors.ftl.
In each I checked if the property name is equal to 'id' and if so, changed it to the name I want, 'comp_id' using something like this throughout.
<#if property.name.equals("id")>
I'm not sure if this is the best way to do this or even the only way to do this but it seems to have worked for me in this case.
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