After Effects + Adobe Media Encoder + Flash = Most Random File Sizes Ever

Asking this question in this AE forum because I think more would have knowledge on the topic here than the Flash Forum. 
I've heard that video compression is more of an art than a science...  Could someone provide me some insight on the following?
-Created a 12 second, 30 FPS, 300x250 banner animation inside of After Effects
-Exported for FLV/Flash to be placed inside of a 300x250 .FLA
-Comps rendered directly from Adobe Media Encoder standalone instead of Render Queue in AE (for 2 pass .FLV's, and heard from various that .FLV's from render queue are not the prettiest at times). 
I've always been under the impression that I would get smaller file sizes with SWF's externally linking to an FLV.  If I do it this way, I end up with: 
41 KB .SWF  + 668 KB .FLV = 709 KB
However, if I EMBED the same 668 KB .FLV to the FLA's timeline (not using the flvPlayback component) I end up with a 381 KB file size!
I am just confused on the logic here, could someone explain the reasons for this?  I always thought my file size would be bigger if it was embedded to the timeline. 

Actually I think it's the tons of extra AS code that make linked players fatter. Never could make sense of the why and how myself, but you can find enough alternate free players/ skins (nonverblaster for instance, which I use) that are a lot leaner.
Mylenium

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