The two era are dead even (with a non-meaningful advantage to modern pitchers) in RA/9. Even accounting for the extra HRs and XBH allowed, once you account for errors, they are giving up the same amount of runs. Deadball pitchers have a very minor difference in W%, one that I expect to even out before the end of this thing. Even now, the difference is equal to 1.3 wins over a full season, so is essentially a meaningless difference (81.6 wins and 80.3 win paces, respectively).
We still have a little season left, and I'd love to run another league to further test this, but I think it's fairly clear the base salary formula does a great job at pricing similar value across the pitching eras. I'd go so far as to say the only difference is preference, and the only reason deadball pitchers seem more popular is because the standard (non-error adjusted) stats don't tell the whole story, so they seem at a glance to be doing better.
In short, modern or deadball doesn't matter, you get similar overall value for your $/IP regardless of era once you account for errors and HR/XBH rates. (That said, I personally prefer modern to deadball because you can draft essentially any fielding grades, where with deadball pitchers to be more successful you'll need to focus exclusive on fielders with good-great fielding and then spend more on defense, forgoing run scoring opportunities.)