If its a photoperiod wait till she is healthy… About two weeks for a healthy plant is fine to let her develop a small root ball. An auto, it is best to just pop them in the container she’s going to grow in.
Regarding the stem… Generally red/purple stems are a sign the seedling stressed (usually overwater or the media is too hot). It depends if she came out with a slightly purple/red tint or she came out with a nice healthy stem and then turned red. If the latter, then that would be a big problem for an auto… For a photo, just adjust and keep growing and she should kick it into gear in a couple days… An auto, id pop another just to have a back up.