I have used the Pro 1000 practically since it was introduced, and have two. First, as to your question: I see no reason why you cannot do as you say, simply by removing the ejector wire and using the location for the size / deprime die for the FCD.
Having said, that, I long ago confronted and dealt with the primer feed issue. As I first experienced, along with some other people I've read about, this unit can feed primers inconsistently. The reason is twofold, and either or both of the following may be involved.
1) the press must be cleaned and lubricated. No matter what the requirements are for other presses, plan on starting a reloading run by removing and cleaning the shell plate carrier and all components. I include here the primer feed channel, which may be readily cleaned with a Q-tip. Then lubricate the points as described in the instructions included with the press; this is an essential step. Plan on doing this every time you reload over 500 rounds or so, or of the press has set for a period of time, even if it's pretty clean.
2) the Pro 1000 feeds primers strictly by gravity, so not only must the channel be CLEAN so the primers can slide, but the "shake bar" that sticks out of the left side of the primer channel and engages the notches in the vertical support nearest the channel must be operational. The shaking action is intended to help the primers move down the channel and onto the primer punch. However, with use, the plastic of the channel can become bent to the right to the point where it will no longer "shake," and thus the row of primers may stall. I solve this problem in the simplest way, by using a rubber band to tension the primer tray to the left, to ensure that the bar rubs against the vertical support, and the shake is consistent. It's obvious, but I might also mention that since the primers feed to the punch solely by gravity, the feed mechanism won't work well unless the primer channel from the tray is FULL of primers. A partially full channel will result in tipped primers.
Since I worked out these fixes, I have negligible problems with the Pro 1000. The last time I reloaded was about 1000 rounds of .40 S&W, and I might have had a tipped primer or two. That's not inconsistent with the results of my other primer feed equipped presses (a MEC Grabber 76 and a Dillon XL 650). The Pro 1000 is an inexpensive press, and is not designed to meet the output of its much more expensive cousins. However, it will produce quality reloads, and its price includes dies and powder measure. For a fully progressive press, it's one of the great bargains in reloading, in my opinion.