Hello!
I am not sure if anything can be done about this, since it's a cross-mod interaction, and relatively niche, but here it goes: Digital Soul assumes that "Automated ships" skill from vanilla is always active when using Second in Command, even when none of the XO's have auto-ship points. Which results in Digital Soul not offsetting the 100% hullmod penalty if you are under 120 auto-ship points, and offsetting a portion that's if you are above.
I have asked the creator of Second in Command, and they have told me that it seems to be possible to change that if Digital Soul checked for auto-recovery instead of the automated ships skill (although I don't really know what that means)