First, I think Acrobat 6 DOES support transparency.
Flattening transparency rasterizes it. You can decide how much gets rasterized and how much stays vector, but your amount of control depends on which version of Illustrator you have, as they have improved this with each upgrade. Also, any text that is in the area of the transparency has a chance of being rasterized. So you could end up with part of a word being raster and part vector. In Illustrator 10 and CS (not sure about 9), there is a Transparency Flattener Preview or something like that which shows as a mask (like in Photoshop) what areas of your art will be affected (rasterized) by flattening.
I really only have experience with this concerning 2-color printing and I know that jobs I have gotten that use transparency have given me a lot of headaches. For one thing, it turns everything involved to CMYK. So if you're trying to print spot colors.... You just won't have spot colors anymore. There are workarounds by changing the spots to percentages of Cyan, Magenta, Yellow and Black but I imagine there are some instances when that wouldn't work. That's what I've had to do to get them to print.
As a prepress person, I'm really glad that you as a designer are showing interest in how to make your jobs print more predictably

I would suggest that you print the seps yourself before you bring in any job to the printer. The more troubleshooting and prepress work you can do, the better. You won't have to worry about some unpredictable color problem, or whatever else may happen. Then you can also bring in your own print outs of the seps for the printer to use as a guide. As a friend of mine would say, "CYA - Cover Your @ss." The more hard copy you can provide, the better. (I love it when designers are prepared!)