1. My site
· Mysite collection master page (root.master) cannot be edited using SharePoint Designer, it actually can be changed but the change is not supported by Microsoft and might cause the site to break. http://community.office365.com/en-us/forums/153/p/58396/213704.aspx#213704
· Feature stapling is not supported as of yet as it is a Farm level feature??? Not sure if this is true but Microsoft do not seem to want to confirm or refute this. It is only available in dedicated online Implementations, not on multi tenancy.
· It is possible to brand the My Site Host and Individual user My Sites with Custom Sandbox Solutions, but this is not supported by Microsoft. It is important to note that when a user provisions their My Site for the first time, it would take default branding based on the OOTB My Site template. The user must then upload Sandbox solutions to apply branding to their already created My Sites. Individual end-users can use SharePoint Designer to update branding on case by case basis as well. This should be avoided as it is not supported http://community.office365.com/en-us/forums/153/p/46010/223145.aspx
· The Microsoft supported way is to use SharePoint Designer to make branding changes or accept the standard themes available.
2. IIS Limitations
· Branding can be done directly via SharePoint Designer or packaged using a Visual Studio project. You start with an empty SharePoint project and add the relevant elements including a feature receiver to apply branding during a feature activated event and retract it during the feature deactivated event. http://msdn.microsoft.com/en-us/Office365TrainingCourse_8V_4
· The master page of a public facing website cannot be changed using SharePoint Designer. Editing of the public website cannot be done using SPD either. All customisations must be done using the site designer tool.
· Master pages for SharePoint online are not set up for fixed width sites or layouts.