Correct. You no longer need to go into the FLV settings to enable alpha channel for output. Enabling the RGB+Alpha option in the Output Module settings is now all you need to do.
One of our goals with the changes made to the export settings in After Effects CS5 was to eliminate the redundancy between the After Effects settings and the individual format settings.
One other note about changes to the export settings - when you open a project or .AOM file from After Effects CS4 or earlier, not all formats will come across with their settings intact; there was an incompatibility between the way the data for the settings used to be stored and how it is done in CS5. Any such output modules will instead default to their previous settings. I can't remember the exact list of formats, but I believe it includes all of the MPEG-based formats. QuickTime and AVI should come across OK. Not sure about FLV but I think it comes through OK.