I'd like to use layman to import only few ebuilds (and all their overlay-deps) from an overlay and sync them later too. For example if I add 'xeffects' overlay, it offers unmasked ebuilds already in portage like qt, cairo, ... and because ebuilds from portage and overlay have the same version I can't mask those from the overlay using the package.mask approach. Alternatively an 'exclude' feature can be a useful workaround to this annoying problem: for example using a config file one can list the ebuilds to exclude from add and sync operations.
See Bug 185377 Comment #4 for solution. (On that note, we are really fed up with bugs concerning xeffects overlay, the maintainer should realize that versions conflicting with official ebuilds only cause lots of trouble to users, public overlays should *never* do such stupid things.)
Jakub is right. This is simply not the way overlays are supposed to work. Any maintainer of an overlay should ensure that there are no conflicts with the main portage tree. Adding exlusion options to layman would be too complex. It is easier to use already existing features of portage such as masking. In addition an overlay maintainer could also split his overlay or you fork it yourself.