Apologies for the delay.
Yes, the Mobile add-on requires Sitefinity layouts. The feature is built around them. Sitefinity can distinguish them among the other page elements and the generated rules apply on. You can also use custom rules which can "play" with any page elements, but that's different story.
I hope this helps. Let us know if you have any further questions.
If the custom masterpages are based on the Sitefinity layouts, there won't be a problem. Otherwise, you should go with your own custom CSS rules.