Developing sites while using Aegir and Drush make
Yes. The short answer is you update your Drush make file to point to the new version of the module you want to be included in your new platform(build).

In your drush make file you would include the version of each module you are including in your platform build. So views for example would look like this.

projects[views][subdir] = "contrib"
projects[views][version] = "3.4"


Now if you want to update to the new version of Views module you would update your make file to something like this.

projects[views][subdir] = "contrib"
projects[views][version] = "3.5"


Then build a new platform in Aegir using this updated drush make file. Then you would migrate the site to the new platform and Aegir will do the update for you.

It's a pretty slick workflow. I keep all of my drush make files in a repo called builds so I can have a record of each build of a project. Hope that helps.