1. Using XenApp to publish applications allow you much more granular control over who gets access to what applications and, if you want to, how maany instances of that application can be run.
2. This one is hard. If you have 100 users needing MS Office, you have to determine the cost of the server hardware, terminal server licenses, XenApp user licenses and MS Office licenses. You could have only 40 people at a time neding to run any particular MS Office app. In that case, do you buy 100 copies of MS Office to put a copy on every computer or do you buy 40 licenses, install it on a XenApp server, set it to only allow 40 instances to run and be done. Also, would you rather update 100 computers with Office updates or one?
3. Citrix does not recommend publishing the server's dekstop. There are some instances where that might be necessary but they are few and far between. Citrix recommends that you use the Web Interface (which is what Citrix itself uses to publish almost 160 apps to their global user base). I have been told that over 95% of XenApp installs use the Web Interface for application access and not Program Neighborhood or Program Neighborhood Agent.
4. From the Admin Guide: seamless window: One of the settings you can specify for the window size property of a published application. If a published application runs in a seamless window, the user can take advantage of all the client platforms window management features, such as resizing, minimizing, and so forth.