This has been a part of speculation for quite some time. and it was suggested/leaked that the bottom row first three slots would go to characters who do not have story modes for one reason or another. This could be for characters who don't have relevant roles to play or it could also be unlockable boss characters. The possibility also exists that the long-standing hole in the center could be filled in by Inferno upon completion of the story, which would be an unlockable boss character and a mimic wrapped into one, so no need for Edge Master.
Talim is confirmed to be both in story and in roster, but due to her age looking relatively similar to her SoulCalibur II appearance, she can only really be the line above Zasalamel, which takes place in 1590.
Astaroth, Cervantes, and Lizardman were all seen in the story trailer and story screenshots that have been released, so those three are definitely safe bets at being both in story and in roster. Astaroth and Lizardman along with Ivy and Nightmare form the Schwarzstrom, and they would all have their roles to play. Cervantes would be killed during the prologue/SoulBlade part of the story, but revival after the events of SoulCalibur but before SoulCalibur II gives him a spot in story too. Voldo is a safe bet at being in roster for sure, since he's literally been in every single game, and is somewhat a mascot. His sub-rivalry with Yoshimitsu also suggests that he will be in story. Tira has story that could encompass this entire timeline, since she is confirmed active as a Bird of Passage starting in 1583 when she was nine years old. Doubt she actually appears as nine years old, probably closer to thirteen-fifteen years old, to be more reasonable, but she has a place both in story and in roster. The last story and roster spot could be either Hwang or Rock, if it's not a new character. I lean towards Hwang, since he has a unique style, unlike Rock.
Raphael, though, his events that you describe about bringing Siegfried out of Soul Edge's control, that doesn't happen until the end of SoulCalibur II, which is in the year 1591. So it doesn't fit on the timeline, so if he is in roster, he could be one of the three that is not in story. Same for Grøh's father, Vergeben has said that he will be a boss character, and if he's unlocked upon completion of the story, since he would be the last last boss, it would make sense if he is in roster but not story. That is, unless he's an overpowered boss like Night Terror, in which case, he may not be unlockable at all. The third and last roster but not in story slot could then go to Cassandra, since she's not really active until SoulCalibur II events either, but there isn't a timeline spot that fits her like Talim. If Grøh's father isn't unlockable, there's also the possibility that Seong Mi-na could go in one of these slots, for the same reason.
We have those two circles in the bottom left and bottom right, tiny circles just off of either side of the bottom row. They likely open submenus.
I'd say one is CaS and one is DLC, personally. The Bonus Characters might be unlockable CaS templates, perhaps, if they don't have their own movesets.