This is information provided by Sarah Mitchell regarding" does Alpha permanently alter the Project when you publish to Alpha for IIS. This question came up during a peer-developer discussion.
I looked into IIS regarding changing your project such that you're locked into IIS.
If you have application security, the way security files are stored under IIS is different from the Standard server. An application running under IIS cannot access security information for an application running under the Standard server. This is probably the biggest difference. The migration guide covers this: http://www.alphasoftware.com/documentation/index?search=iis%20migration%20guide
That being said, this is only for published applications. You can define users and groups in the development environment. Security settings are deployed to IIS at publish. So, this should allow you to publish either a web application using either IIS or the Standard server without needing to maintain duplicate copies of your project. This is from our IIS Migration guide:
When users and groups are defined in the Web Security settings in Alpha Anywhere Developer Edition there are two options for storing the users and groups: DBF and SQL Database. When SQL Database is selected, users and groups of a production application can be managed through the Alpha Anywhere Developer Edition or by pages in the application that are usually restricted administrator level users. This is no longer the case with IIS since a deployed application's security data is stored in IIS provider specific database tables. The users and groups stored in the DBF or SQL Database are published to the IIS provider specific database tables at application publish time or by way of the "Publish Security Files" feature in the Alpha Anywhere Developer Edition Web Security control panel. Day to day user management (such as adding users, disabling users, resetting passwords, and adding users to groups) needs to be done by administrator level pages in the application.
Specific changes were made to Alpha Anywhere in version 11 to allow a web application to run under both the Standard server and IIS application sever without needing to make changes (http://www.alphasoftware.com/documentation/index?search=iis
overview). This included the deprecation of some session variables and the introduction of the Context object, which can be used to access the session and request objects in xbasic using Context.session and Context.request, respectively. Context will work in both a Standard and IIS application sever deployment.
As far as other settings, however, I am unaware of anything that would make your components unpublishable to a Standard server if you deploy them to IIS.