First, the prestige classes are exactly the same as the base classes in this regard. You would get the same effect by multiclassing to the sorcerer as you would by multiclassing to the master specialist.
What an effect East is in place for at least one debate. There are two major formal approaches to managing this, plus a very common rule that is at the heart of your concerns.
The simplest approach, which I will call the "first round" approach, is simply to read the numbers on the table and add them up. This means that you get +2 in your will when you take your first level of master specialist, yes.
I call it "round first" because the numbers in the table are already rounded for you – a wizard earning ½ point Will will save each level, but the table does not show that at odd levels, it just shows a gain of 1 every 2 levels. Your base will save your wizard levels is really + 3½, and the master specialist really adds + 2½ to the 1st, but you round these to +3 and +2.
The other approach, the "last round", also known as the "fractional", Arcana Unearthed calls it, requires processing these fractions. You add + 3½ and + 2½ and get +6. Regarding your concerns, this may seem to make matters worse, but consider bad backups: it is quite common to play a second level barbarian / second level fighter / second level ranger (the basis of a construction to tripple over the horizon). At the 6th level, this character has two levels in each of the classes which all have low willpower saves, so + ⅔ + ⅔ + ⅔. If you round up first, it's +0 +0 +0, when the lowest 6th level character should ever be +2. If you round last, you get exactly this + 2 – which is the point, rounding the latest results to multiclass characters more similar to those in a single class.
However, as you can see, this always results in the assistant / master specialist getting a will that is too good. An extremely common rule – especially during the last rounding – is that you can only get the +2 the first time you get a good save. So the fact that your sorcerer has already obtained the +2 will from the 1st sorcerer means that he does not get it again at the level of the master specialist 1st, therefore + 3½ + ½, for +3 if rounded first or +4 if rounded last. Since +4 is what a level 4 assistant would have been, in my experience, considered to be the ideal outcome. The asymmetric save shots that come from rounding first and repeating + 2 are really bad for the game.
But it all depends on the DM; you will need to ask them which rules your game uses, and all characters – PC and NPC – should use the same rules.