It can, you simply have to put them in the top left slot (or middle, I forget).
Why not just use the fluid output upgrade instead? No piping needed.
Yes, I noticed that later, but still had to make somewhat of a contraption to pump the CF that I had already enriched back into the left tank, and later I noticed that all the content of the right tank gets automatically inserted into the container with the next operation... Well, at least I didn't lose anything in the process, except for time, which isn't that much of a matter considering I'm spending it on a game Took me a good hour or so after posting here to figure out how the new machine actually works, and that's only for CF still...