The presentation I typically use for the last phase of my 3-Fly routine is to place the last coin to travel into my pocket. This is a quick and clean presentation, but it can arouse suspicions and it isn't very "flashy" in my mind, even when having the coin travel to a spectators hand. It doesn't have to be flashy, but...

I am wondering if performing a simple coin in small paper envelope vanish would work nicely to give the last phase a little kick. I would think using fire and flash paper would be ideal. My biggest concern is that it could possibly slow the 3-Fly down to a crawl, and it isn't as immediately clean.

What do you think? Have you done something similar?

In my opinion, the reason 3fly routines work so well is that there are no outside items used, it's just the coins and the hands only.
The only way to find out if what you're thinking works and gives the reactions you hope for is to try it.
Video it and watch the video. It may look good it may not, trust your instincts.