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It should work something like this:

tell application "OmniPlan"
	tell front document
		save in "Volumes:Extra:myReport.htmld" as "HTML Full Report" with properties {export template:"Users:lizard:Library:Application Support:OmniPlan:HTMLTemplates:Custom Project Report"}
	end tell
end tell
However, that's giving me an error right now. I've filed a bug, and hopefully we can get an engineer to look at it soon. (But feel free to try something like this anyways and let me know if it does somehow work for you.)