CS4 RENDER vs Media Encoder

Hey Guys-
Thanks in advance for all of the help that you provide on this forum.

My Question:
In short, I'm using AE-CS4 for composting a video that eventually needs to be an F4V for display within a Flash Container.
I should mention that I have all of this working, but am questioning all of the encoding/re-encoding steps I'm performing to get there, and which best practices to follow.

Here's what I'm doing:
(1) I have HD (1080p) footage that I'm using Handbrake to convert to H.264 (mp4, m4v). I'm doing this due to the challenges with AE-CS4 and HD Video.
(2) I import the H.264 footage into AE (CS4), add other elements, and RENDER to F4V format
(3) From there, it's gravy (FLASH).

Does it make ANY sense to RENDER (in step-2 above) to .MOV, then use Media Encoder (and it's additional settings) to render to .F4V? I read that somewhere and don't quite get it.
Or is that just plain stupid?

My goal (as everyone's is) is to gain the highest quality that I can. BTW...the Web Page that this stuff will be shown in is on my company INTRANET, so bandwidth is not a major concern.