In Rashi, eruvin 56a, nine and ten lines from the bottom, does the aleph at the beginning of the abbreviation stand for chatzos? If it does, then it would seem to be inconsistent with the remainder of the abbreviation.
You are making an excellent point. It must be that Rashi did not want to use two letters to refer to the hour (that is, Y"B (Yud Beis), which is the more accurate representation of Chatzos), in order to prevent the abbreviation from becoming confusing (one might read Y"B, or 12, as Y (10) and B (2)). Rashi was not concerned that using the Aleph would cause people to err, because it is clearly understood that the Aleph refers to the beginning of the first hour and not to the end (like the other letters), since it is the very first letter in the abbreviation.
(It does not seem correct to say that the letter Ches should appear in place of the Aleph, referring to Ch atzos, for we do not find such an emendation in any of the earlier printings or manuscripts mentioned by the Dikdukei Sofrim.)