Hi,
The first setting is for actually forcing medium trust when testing. You would never use that setting on production.
The second setting is to let mojoPortal know it is running in medium trust so it can handle things differently where needed.
I've just updated that document. The thing that doesn't work in Medium Trust is the VirtualPathProvider that reads the theme.skin file from the skin folder. Since we really don't use the theme.skin for style its not a huge problem. The only settings we use from that file are for our CornerRounder controls which can be either enabled or disabled using the theme.skin file. The control doesn't actually round corners it just adds some extra divs that are used for corner rounding by css. But in some skins where corners are not rounded this can be false to eliminate those few extra divs. The extra divws don't really hurt anything though. In medium trust it just means you can't set it per skin, its global setting and it comes from App_Themes/Default/theme.skin instead of from the skin folder. All the other skin files come from the skin folder and don't need use of a VirtualPathProvider.
Hope it helps,
Joe