My baby is 11 months old and has hypotonia and plagiocephaly. He wakes frequently at night when not "swaddled" or held. He has only just started rolling but is expected to roll more and more in the coming months. Is there a "safe" way to swaddled or nest him in bed so he can sleep better and with more support?

Red Nose generally recommends to cease wrapping once baby is rolling, as baby needs to have arms free to roll safely.
Maybe you could try using a sleep bag with arms free, which still gives some degree of support.
Do you have a specific management plan for your baby?

Red Nose also recommends the following when baby is rolling.
Give baby extra tummy time to play when awake and supervised as this helps baby to develop stronger neck and upper body muscles which in turn enables them to roll back over.
Make sure that baby is on a firm and well-fitting mattress that is flat (not tilted or elevated).
Make sure that baby’s face and head remains uncovered (do not use lambswool, doonas, pillows, cot bumpers or soft toys)

As babies grow and develop they become very active and learn to roll around the cot.
At this time, continue to put them on the back at the start of sleep time, but let them find their own position of comfort.
By this stage it is not necessary to wake during the night to turn baby over to the back position

Do not use any devices designed to keep baby in a particular sleep position.
https://rednose.com.au/article/what-do-we-do-now-that-a-baby-has-started-to-roll-over