My goodness that sounds like a useful tree (
Ken Fern's info here for those like me who are not familiar with it.)
The seedling looks pretty healthy to me. If it is naturally opening and closing, I wouldn't cut off the cotelydons as you may damage the plant tissue and lead to disease. I assume the true leaves can take (or even need) this movement, or maybe it protects them from overnight nibblers....
I'm not sure about the stem colour. It is possible this is the first signs of a stem rot, but it may be just the stem maturing. Not much you can do at this stage other than try and avoid overwatering I think. Maybe water from underneath for a few days if you think it needs it.
Well done for getting a seedling! It looks like the seeds do need careful (cool) storage to remain viable for any great length of time. I do hope that this one makes it!