If you start with a Facing Page document, the side-by-side pages should not overlap when you create an alternate layout either wider or narrower.
With Facing Pages unchecked, if you dragged the pages next to each other they will overlap or have gaps.
If you have facing pages in a spread you have to set up your document with facing pages. If you don't, you can't use any style which is related to the spine, as anchored frames in Object Styles or paragraph adjustment (most likely used for page numbers and running headers on the master) in Paragraph Styles.
Steve and Willi - thanks for the input. Using facing pages isn't really an option for my users. They don't utilize half of the functionality I build in (paragraph/character/object styles, running headers, TOC,etc.) and facing pages introduces issues they can't handle. The fix appears to be continuing to split the spreads (before or after creating the alternate layout) and then putting them back.