New problem (what I was trying to avoid, with Kate) is that pasting contents back in messes up all indentations.
Regarding "copying the entire windows in XML format", can this be pasted back in (safely)? Is that what rest of this posting is about (serializing and de...)?
Ignition's editors use tab-indentation and a tab width of four. Place a kate modeline at the bottom of your scripts to make kate conform.
Copy entire window out as XML, edit, and paste entire window back in as XML. As long as you don't disturb the structure of the object references, it'll work.