The pro-level bleeding tools are pressure-bleeders that fill/flush/bleed and even help in testing for leaks. The preferred method.
The fancy ones do have an internal diaphragm to separate the fluid from air, but one isn't going to find that on a DIY-level tool, which more mostly glorified garden sprayers.
I have a Motive, which has a pump to generate pressure, as well as a Gunson, which relied on an external air source (a tire) for pressure, like the Speedibleed.
The Motive is ok, but anyone who has owned a consumer-grade garden sprayer knows that they're not exactly built to last.
In use, I actually preferred the Gunson, which had more, and more consistent pressure from a tire, which is also easier to set, and refill to a preferred PSI level. It consistently filled the reservoir while under pressure, and didn't leave a large air bubble like the Motive does. However, though the principle is sound, the execution and build quality left something to be desired, with leaks at the tire chuck, and the reservoir adapter cap. The dealer was good at support with replacement parts, but fighting the tool got tiresome, which is why I bought the Motive for cheap online when things were still practically being given away to build online commerce.
No matter which style, the most vital part of a pressure bleeder tool is a good adapter cap. That's much easier to achieve with a threaded cap, like the style ATE has been using forever; I'm glad I don't have to deal with any vehicles that have the snap on covers like GM has used in the past, and such.
As far as whether to fill the bottle, in my mind, I'd much rather have the hassle of cleaning the bottle, rather than risk pushing air into the system and having to do the job again, especially if it involves a clutch, which can be more problematic to bleed.
Cleaning the bottle is another task, but again, I'd rather do it right, and start with a clean slate 2-3 years down the line, rather than pour fresh fluid into a container that has remnants of old brake fluid, not from a sealed container, and push that into the system the next time.
If I had to do it now, I'd probably opt for the Speedibleed, and will when the Motive acts up.