Forget what I said about Sierra's skill, it wasn't a bug , I have done something that wasn't supposed to be done , and now , the Dev of SOTF is working on a future neural intégration with Sierra. But it would be nice if you could check eachother for futur compatibility.
But your mod definitely change something with neural link ( probably for the best in terms of balance). when your flagship left the battlefield, if you transfer ( by using the link) to your second ship before the first leave , you still benefit your skills without having to physically transfer to the second. This is vanilla
But with your mod , you can't do that , you need to physically transfer to your ship, which make more sense, even if I miss something the abuse of vanilla.
Also the phase milestone which allow you to not suffer phasecoilstress is lost when you physically transfer to a linked ship ( not saying it's a bad thing , just a notice)
Last , how to unlock milestone when you add this mod in midgame? for me , even after Finishing the main quest , some of the milestone don't show up.