I think the judge probably believes EA's own statements to police combined with the DNA evidence should be enough to convict.
So, maybe in the judge's mind, if the jury sees how small the trunk is:
-it could be more likely to sway a weak juror that she couldn't have fit in; or,
-given what is already known, it's just overkill that will confuse a weak juror further.
Other than that, don't know why he'd make that comment. Can't think of a specific legal reason it would hurt. But, could easily see a juror second guessing him or herself after seeing how small the trunk of the car is.