The Adobe AIR Settings Manager should be working with AIR 2. I tried disabling the popups with 1.5.3 installed and it hasn't prompted me to install 2.0.2 yet (on Mac). Are you finding that it ignoring your setting?
Yes, it happened in Linux and Mac installations.
We will try to reproduce this problem at our end and let you know as soon as we have any update.
Btw, which Linux distribution are you trying?
Could you once run the app using adl (AIR SDK) and see if there are any errors you are getting. I tried on my Linux Ubuntu 9.10 machine and the AIR settings manager worked perfectly.
An alternative approach on Linux could be to do the following:
sudo vi /etc/opt/Adobe\ AIR/globalRuntime.conf
or create the file ~/.appdata/Adobe/AIR/updateDisabled
This will block any automatic runtime updates on your system.
We are using Ubuntu 9.10.
Could you try downloading the AIR 2 SDK from : http://www.adobe.com/cfusion/entitlement/index.cfm?e=airsdk
and run the AIR settings manager application using adl.
You could extract the SDK to some folder and then run the following command:
bin/adl /opt/Adobe\ AIR\ Settings\ Manager/share/META-INF/AIR/application.xml /opt/Adobe\ AIR\ Settings\ Manager/share/
Do you get any ActionScript errors?