Has he done so?
and under the UCMJ is he allowed to do so?
While I can't say that I'm familiar with all, or even many of the birther cases, I don't believe a single case has survived a motion to dismiss, as such, there haven't been any other motions presented nor have their been any discussions about stipulated facts. These are things that happen after a judge has decided that there will be a trial.
"and under the UCMJ is he allowed to do so?"
If the military judge rules that the events surrounding Obama's birth are relevant to Lakin's court-martial, the yes, the prosecution could stipulate those facts.
From everything I've read though, Lakin wouldn't be interested in such a stipulation because he believes that Obama was not born in HI.