It may work somewhat without those as long as the content place holders have the correct ids, but there is some logic in the code behind for layout.master that is looking for those divs with those ids. The logic is not doing anything really important, it just adds a css class "cmszone" to the divs and this class is not currently used in any included skins so it really isn't very important. Basically all of the content wrapper divs have this cmszone class so it could be used to apply styles on all content regions. So really the cmszone class is designed especially for the case where you are using these 2 extra regions and you might need a way to apply styles that affect all of them. Of course if you use a different id for the alt divs then you could manually add that css class if you wanted to.
<asp:ContentPlaceHolder ID="altContent1" runat="server"></asp:ContentPlaceHolder>
<asp:ContentPlaceHolder ID="altContent2" runat="server"></asp:ContentPlaceHolder>
Let me emphasize for other readers that though the div id is not that important for the 2 extra content sections the ids for divLeft, divRight, and divCenter are very important. For consistency I think it is better if people just think of them all as important.