It is a common practice to use a separate module in a multimodule project just for assembling the zip. There's also the appassembler-maven-plugin which might be interesting for you (I've never used it myself, though).
About running a plugin without a phase: that's always possible. Execute the full name as specified on the goal-page. In this case org.apache.maven.plugins:maven-assembly-plugin:2.4:single
, or in short assembly:single
.
Don't try o solve this with profiles, they aren't meant for that.