As far as I understand it, the VBD baselines in the draft dominator have completely fixed values, so it makes a lot of sense to adjust them to your individual league scoring/settings. It's actually one of the weak point of the draft dominator in my eyes, it should be able to determine the baselines itself based on the league settings.
I aggree with snoochieboochies that simply taking the #12 player is not the way to do it.
In a 12 team league starting 1QB , 2 RB and 3 WR, the starting player baseline should be the 12th QB, the 24th RB and the 36th WR. You can either take last years league results, or take this year's projections to find their scores. If you have flex positions, you got to split it up between 2 or more positions in a way that you think will happen. Often, TEs aren't used at the flex position for exemple. In very standard leagues the number you will have will come pretty close to the one set by the Draft Dominator, but in exotic scorings, especially 2 QBs , Superflex or 2 TE leagues, the baseline of those positions will be way lower than the set values, resulting in the players having more "value".
As far as the worst bench baseline goes, you will have to guess how many players will be rostered at each position. If you think everybody will roster 2 QBs, than it's the #24 QB as the baseline. In 2 QB leagues you can expect every QB to be rostered for exemple, so the number will be pretty close to 0.
When drafting, the "rostered player baseline" becomes more important during the second half of a draft, when you fill up your bench. It clearly indicates which position is harder to find on the waiver wire during the season.
Unfortunatelly, if you override the baselines in the draft dominator while drafting, it overrides the values in all your active drafts. It's also always reset itself to the standard values everytime you closes it.
tl,dr: you can keep VBD baselines in standard format leagues, but absolutely need to change it in exotic formats.