1.) You are not asked twice for the same thing.
I can remember in a past version of PDF Creator (about 2006 or 2007) there was only the one check box in the feature list. If you said yes, then the toolbar is installed.
The second option that you get prompted asks, if you want to make Yahoo your default search engine. If you really want to use the toolbar I think it makes more sense that you do not make yahoo your default search engine because for this you have the toolbar.
2.) Most people find this toolbar annoying, but I prefer having a free software on open source basis with a toolbar then a software for 30$ per installation without a toolbar. This is the other way to get money for the project.
If I would have paid for PDF Creator I would not accept this toolbar, but so it is OK. I know that there is a little trick to get the people installing it, but in other software you do not have the option to turn it off.
3.) If you dont want the toolbar and you have already installed it you can remove it from Control Panel => Software very easy. It is also not a big deal to hide the toolbar in your browser.