Certain changes can be more easily explained than others, like the difference between the carriers and ARMD on the Macross. Since the Macross was heavily damaged at the end of the Macross tv series, it is quite possible that they decided to replace the carriers with the ARMDs when the Macross was rebuilt.
Other changes are not so simple....
i perfer a more real world explaination. either 1. having armds instead of naval ships makes it more sci-fi and/or 2. it looks cooler.