Spells are still chosen by rolling for one wizard at a time. You get to choose when a duplicate spell is rolled and then that wizard can swap a spell for the signature spell. You then do the next wizard the same way, but each one from the same lore is going to get easier to choose as duplicates will come up more. Since each spell can only be taken once (sigs aside) if you take a level 2 and a level 4 of the same lore and have the level 2 roll for spells first and using the signature spell to push a spell you want for your level 4 off him, you can pretty much guarantee your level 4 gets the spells you want.
Sunny is pretty much saying he prioritizes 1) Raise Dead 2) Van Hel's 3) Invocation 4) Curse of Years/ Gaze of Nagash (I agree with this prioritizing btw). So if he rolls and gets duplicates and doesn't have one of of those higher priorities, he would choose in this order. It also means if his level four ends up with hellish vigor and the rest these above, he would dump HV for IoN.