My youngest (DTs) were 3 when we separated. Also had a 5 yo and an 8yo.
He lived 3-4 hours drive away.
We agreed eow. But the DCs found the long drives arduous and complained (more the older 2). Occasionally one or other of the DTs would cry and refuse to go, but I don't remember them being distressed or particularly unsettled on return. for the younger ones it very quickly became their new normal.
In relation to distress at handovers, XH was quite sensible and would offer to leave a DC behind if they were crying and not wanting to go. I didn't want to establish this sort of pattern and so would encourage him to take them all, and reassured him that any distress would be short lived (which it always was).
I was lucky that I had a very reasonable ex who listened to me. When it was obvious they hated the long journey, I asked him if we could rejig the arrangement - either he stayed locally to me in an Air bnb occasionally, or we changed to every 3 weeks. He chose the latter. We never went to court or came close to it. As the children got older he realised that they would want to be near home (eg for sports matches) and so for the last few years he has stayed in an Air bnb with them (if I'm away I let him stay in my house). The younger 3 are now 15, 15 and 16.
I get the sense from your post that your ex won't be like mine, so any discussion about rejigging arrangements will be a no go. It's too soon after the court order to seek to change it.
I think that DD will settle into the routine once it becomes her new "normal". Be aware of your own stress of her leaving and relief when she returns, and don't allow her to pick up on it. Why is she unsettled?
Is she tired? Clingy? Maybe she going to bed too late and you could raise this with him? Or is it because she is sleeping in the car and reacts badly to being woken up, and then has her bedtime disrupted as a result (which wouldn't be surprising)?
If the problems are more deep rooted, then you need to start laying down markers about it now in case you do decide to try to vary the arrangements. However, I think it's unlikely you'll end up with less than eow and the court's view will be that DD will get used to it if both parents support her.
I wonder if a lot of this is the long journey and her sleeping in the car which is then making her grumpy and unsettled. Not an awful lot you can do about that (except maybe change the time she is brought home to an hour earlier?), particularly with an unco-operative ex who doesn't have to deal with the fall out. Give it a little longer and if the problems persist try to see if he will change the time he brings her back (which you can then agree to review when she is a little older).