If you publish a Clickonce application from within visual studio, it will generate publish.htm .This seems to be Visual Studio generated, and not part of the publish target
I use batch scripts with mage.exe to create my manifests and publish page. Updating the publish.htm page is trivial. There's a section in the HTML file that looks like this:
Name:
AppName
Version:
1.0.0.0
Publisher:
AppPublisher
In my scripts, I just have that "basic" publish.htm file as a template, and I do string search/replacement for AppName, 1.0.0.0, and AppPublisher with whatever values I want to plug in.
Also, if you're not familiar with mage.exe, I'd check out MageUI first, then get your mage.exe scripts written (if you're going to be doing this more than once or twice).