Hi,
1. no currently sites are completely independent unless they use some common external user source like LDAP or Active Directory
2. I cannot ship the MS Ajax dlls with mojoPortal and I don't think they can be used on Mono so I avoid dependency on them. However I have the ajax-extensions-pak download that replaces a few mojo files for those who want to use MS AJAX to support the WebPart drag and drop in Firefox. This site is configured that way and has the script manager in the MyPage.aspx page. If you want to use the MS AJAX stuff in your custom modules that you develop to plug into mojoportal you can move script manager out of MyPage.aspx and into the layout.master file in your mojoportal skin.
mojoPortal already uses some non MS ajax techniques for a few features and recently I added all the open source javascript files from the MS AJAX and AJAX Control toolkits under ClientScript/msajax so they can be utilized as well. I implemented a CornerRounder control in mojoPortal.Web.Controls project for example which uses the same javascript as the similar control in the AJAX Control toolkit but has no dependency on the MS AJAX dlls so it can also be used on Mono.
3. Don't know much about nested master pages myself, haven't used them. In mojoPortal master page is just one element of a mojoportal skin (not the same thing as theme.skin thats only a part of mojoj skin as well) mojoPortal allows specifying different skins for different pages and they may achieve some of the same results in some cases.
4. It runs on 2.0 .NET and uses many of its features where needed but not just for the sake of using them. I don't really know what you mean supported, it supports mojoPortal, mojoPortal doesn't support it.
5. Item 2 on this page:
http://www.mojoportal.com/creatinganewfeaturemodule.aspx is a Flash movie tutorial that is basically the start of a new feature and equivalent of Hello World.
mojoPortal is a content management system where pages are represented in the db and the main real page is Default.aspx in the root of the site which actuall displays all content pages using the query string param pageid to determine which page to show. We use url re-writing so you don't see the query string param in the url.
A mojoPortal module control is basically a UserControl with a few more features built into the base class. your custom modules can inherit from SiteModuleControl and then be able to plug into the content system by being placed on a virtual page. More elaborate features often do require additional .aspx pages but these are outside the menu and linked to only form within the module control. Of course ecven with these pages your functionality could be encapsulated in user controls or web controls.
Hope this answers your questions.
Joe