No.
If you tell it your prime output, it creates settings based
on that. You can still produce any of the other outputs from
whatever you select but there will be some simple changes.
Principally, the window options are different for CHM and webhelp.
If you create a new window, it is based on your default layout but,
as I said, you can always change that.
Help others by clicking Correct Answer if the question is answered. Found the answer elsewhere? Share it here. "Upvote" is for useful posts.