Creator of Howl here, so everything I'll say is going to be a bit biased.
It is possible to build multiple files with a shared code base (such as a client/server model). I
use this in busted to build both an executable and an API.
It wouldn't be hard for me to allow the combiner to depend on a combined file either - most of the dependency code is there already. The combiner can now depend on a any build artefact, such as another combined or minified file.
A key thing to note is that whilst Howl comes pre-packaged with a host of existing tasks, it isn't much of an issue to add your own. So if you need to do something special it is easy to add some a custom task and get all the other benefits of Howl (such as minification). This means if you want to use something like BombBloke's Package then you could minify the files and then have package them all within Howl.
On the disadvantage aspect, I guess it is more setup for developers, but apart from that I can't think of any. If you do choose to go the Howl route, and come across issues do PM me/put something on GitHub, I'm generally pretty fast with bug fixes.
Edited by SquidDev, 15 September 2015 - 08:30 PM.