1. align to safe spot is a new feature comming within a week, for the paying customers atleast.
Secondly, whats going wrong for you. is that your super takes to long to enter warp, and there for thinks it's stuck on something. theres a setting for how long it should wait before expecting warp. I think it's in the OCR settings. it's on zero and putting it at 20 or 40 might be what you need.
I had the same issue in my carrier, but the OCR setting fixed it for me. And I trained Capitals to lvl 4 to get better alignment speed.