The new out-of-game patcher has a checkbox for 'restart when finished' that will mimic the old patcher's behavior, restarting HoN once the patch process is complete. This option is on by default.
I've only managed to test this twice, but as far as I can tell, if you uncheck this box, HoN itself will not recognize that the patch was applied correctly, so next time you manually start the game it will begin the entire patching process over again.
Going to confirm
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Look for my highlighted text (important information) and grey text (interesting but not required information).