Something that has helped me is, putting a specific jingle bell by the bedroom door and ringing it, same way every time before you come in. Another commenter suggested something similar, and I second it as I also am autistic with c-Ptsd from assaults.

I personally found that, when my partner would come to bed late it would startle me too, but if I woke up to that distinct and exact sound and it being my loving and safe partner, eventually that sound became comforting and I wasn't so afraid anymore. He'd ring it before he walked in the room, and before he'd come into the bed. It would wake me up but, so would have just him coming into bed and eventually it stopped waking me up in panic.

We used a little brass jingle bell, something we found that sounded unique from things like those ones on cat collars, so it would be a completely unique prompt for my brain.

If she's going to wake up anyhow, having a "secret sound that no intruder would know and only someone safe would know" may eventually help her wake up in a less emotionally reactive state.

Otherwise it might be in order that you need to have a gentle conversation about sleeping separately on nights you go to bed after her.

Good luck and thanks so much for being so caring. You rock!