Yes, it is safe to attach a battery directly to Vsys, as long as the voltage is within the range specified in Custom Expansion Board Tips there should be no problem with your Edison.
Honestly i didn't make any measure on intel board on Vsys when battery connected. I also try it in another PCB, and inRush current was high enough to halt edison boot. Maybe LTC4067 or BQ24074 reduce this effect.
I estimated that LiIon battery has internal resistacence of 80mOhm.