You can Mate to sketch entities. I do it often. Where is this 3d sketch? Is it in the Assembly, or does it belong to another Part in the Assembly?
Edit: I didn't see the part about mate references. Sorry about that.
I am going to say it is not possible, this based on my experience recently where I was not able to use anything other than actual geometry for mate references. I was trying to put in a split line and setup the mate reference to that but it wouldn't let me.
It is possible, and it is very desirable. I always do it and why you do not can do it ?
You may snap your parts to sketch made in assembly or to sketch that belong some driving part taken in the envelope or to sketch that belong to part saved inside the assembly.
Inserting in assemly driving part taken in envelope is the best as for me. So you can manage your assembly by simply editing the driving part.