G'day flynnkd
There are a couple of reasons for the dummy PIP dice (and if you have four commands, no you don't get a 5th PIP dice).
First, depending on what other stratagems you might use, it allows you to deceive your opponent about whether you actually have a fourth command.
Second, it ensures (at least for a while) that weather effects occur equally for both players.
And now to expand on these a little...
First, imagine your opponent deploys two commands on table, and there are clearly less than 400AP (or whatever) of visible troops. When he rolls four PIP dice, you don't know whether he has a double flank march, or a single flank march plus a dummy PIP dice, or (confusingly) only two commands with a lot of troops hidden somewhere on the table and two dummy PIP dice. This makes it harder for you to deploy troops to pre-empt what you think he's done.
For example, I had a game where I used Early Crusaders against Fatimids. I deployed two commands on table - a very large Crusader command under the C-in-C, and a Byzantine ally. I fortified my baggage and used the Delay Battle stratagem to improve my chances of any flank marches coming on. My opponent, on counting the points of my on table troops, could easily assume I had only a single flank march of modest size. In fact I used the Exaggerated Numbers stratagem to make the C-in-C's command look big, and had two modest-sized flank marching commands. (The story of the game is on the forum here somewhere - entertaining reading if you're not the Crusader player, as everything went wrong...)
Back in the days of DBM, you only rolled as many PIP dice as you had commands. This usually meant you knew whether your opponent was flank marching (or at least, it was a lot harder to mislead opponents than it is in DBMM). And in cases where the terrain made a flank march on one flank impractical, it allowed the opposing player to set up a response to the flank march well before it arrived. This was unrealistic and gamey.
Second, there are a variety of weather effects (for examples, wind direction, rain starting and stopping) which occur when your - or your opponent's - PIP dice average more or less than a certain amount. Those PIP dice averages are more likely to occur the fewer dice you roll. So if you roll fewer PIP dice than your opponent, this leads to the odd situation where those weather effects are more likely to occur in your bound than in your opponent's bound.
So making both players roll four PIP dice at the start of the game means that, at least for the first part of the game, weather effects which can occur in either player's bound will have an equal likelihood of occurring in your bound and your opponent's bound.
Does this help?