Doctypes are in the simplest sense a detailed description of a set of commands and how they should be interpreted. One doctype may have commands that another does not. It may have the same commands but interpret them differently from another doctype. Some parts may be exactly the same (this is something like spoken languages.) SS/SSP use a specific doctype and then writes all its HTML and scripts using only that doctype so that we can guarantee that a page will look exactly (or as close as possible) to what you placed in the workspace.
If you change the doctype, the browser will interpret the HTML in a different way. It will not likely be in the way SS/SSP (or you) intended (like you started speaking English to a French only audience. They may get an idea of what you mean but they will probably get it mostly wrong).
Other people create scripts using the doctype of their choice. If you want their script to work exactly as they intended you have to use their doctype. If you mix their script with the SS/SSP output, and their doctype is the not the same, you will get mixed results. You can use either their doctype or SS/SSP's, but not both on the same page - it will be wrong for one part or the other.
At the time SS/SSP was released it used the most prevalent doctype. In a future release it will use whatever is the most prevalent doctype at the time. It's code generation will have to be rewritten to match the new doctype.
You can change the doctype in an SS/SSP page so that it matches the type used by your script (LarryD has a useful tool for this here) but it will no longer match what SS/SSP produces and you may see problems in the way things are displayed.
Update: There is a new ‘doctype’ option (as of 2.92e) for the code object that can be used to change the doctype on a page. Then use the following (from the popup tips text) to describe how it works.
Selecting 'Doctype' in a code object will cause the contents of this object to replace the standard doctype in the HTML output. It will not change any other code therefore you will have a doctype that may not match the rest of the generated HTML. This may cause unexpected behavior on the final HTML page. Do not use this option unless you fully understand the implications.
Right-click in the doctype code object with your mouse to choose a pre-defined doctype or type in the text you want. The text will be used exactly as it is to replace the existing doctype.