From the look of the files in the setup edition, it seems like Gluu 2.4.4 does support idp3. But in the installation process, it's not asking any questions related to idp3 (meaning whether to install idp3 or 2).
In setup.log, the line Install Saml Shibboleth IDP v2 is found.
Is there a way to command Gluu to install IDP v3 install 2?
Actually, Gluu 2.4.4 doesn't support IDP3. But the next version of Gluu will which might be released in January 2017.
From Gluu community
No, support for IdP3 will be added in Gluu CE 3.0, which is in final stage of development.
Update: to be exact, it's possible (I've seen some builds of 2.4.4 with it, for internal usage), but without web UI integration. Still, such custom builds won't be covered by Community support, unfortunately
https://support.gluu.org/installation/3572/how-to-install-with-idp3/