JL-2 is already almost same size as Trident II and diameter wise larger than original Trident I. Is there any reason why 10.000km range JL-3 wouldn't fit on 094A? I mean French M51 is shorter than JL-2 by one meter but is more capable.
You have to be careful about comparing the missiles along just one dimensional parameter. The M51 (12m long with 2.3m diameter) is volumetrically the largest missile (around 50 cubic metres), followed by the Trident II (13.41m long with 2.11m diameter) at 47 cubic metres, followed by the JL-2 (13m long with 2m diameter) at 41 cubic metres. Being "skinny" is a very undesirable trait in a missile given that volume scales quadratically with diameter.
Yes, there's a reason a larger JL-3 wouldn't fit in a Type 09-IV launch tube - if the tube could fit a bigger missile, the JL-2 would be a larger missile.