First, you'll have to export from Flash as something other than .flv. Avi, .m2v, .mpg, .wmv and .mov are acceptable for import into Encore.
But if Flash won't let you export in rectangular pixels, then that won't matter. You will need to import your Flash video into another program like After Effects so that you can export 720x480 0.9 PAR.
With 720x540, you will have to scale the video in AE to 89.9%. If you use a 648x480 square pixel Flash project, then when you drop it into your 720x480 0.9 PAR AE comp, it will be scaled automatically and correctly. Then export to .avi or mpeg from AE for use in Encore.