It could be because it would prompt a huge pain in the ass process or question of, does their discharge status change? Granted, they dont (at least not during my service or my dad's, to give context I served 2013-2018 and dad 1995-2003) give our dishonorable discharged. But a general discharge or other than honorable (OTH). If these are pardoned UCMJ violations that lead to a discharge, does it prompt to change their discharge from OTH or General to Honorable?
My guess is also the UCMJ is like a separate court system out side of the usual court system. Since military are held. to a 'higher moral standard' and such. Even if it were made legal for citizens, it may not mean military rules are amended to allow use. An example could be Spice. While you could buy spice at a head shop and smoke it, not illegal, the military deemed it against the rules and you could get kicked out for smoking spice.
First, let me say that I think your comment is fantastic. Not that many people have the capacity to think through military justice issues in all their nuance. New convening authorities often have a more tenuous grasp of the interplay between courts-martial and discharge characterizations than you just demonstrated.
There's potentially some question as to whether the President has the power to pardon the conviction and impose an OTH, because an OTH implicates a liberty interest and requires a hearing unless waived. See, e.g., Vierrether v. United States, 27 Fed. Cl. 357, 364 (1992), aff'd without op., 6 F.3d 786 (Fed. Cir. 1993), cert. denied, 511 U.S. 1030 (1994).
However, I'd be hard pressed to find any objection to unilaterally imposing an administrative discharge with a General (Under Honorable Conditions) characterization. Alternatively, there is nothing preventing the President from making the pardon conditional.
My guess is also the UCMJ is like a separate court system out side of the usual court system. Since military are held. to a 'higher moral standard' and such. Even if it were made legal for citizens, it may not mean military rules are amended to allow use. An example could be Spice. While you could buy spice at a head shop and smoke it, not illegal, the military deemed it against the rules and you could get kicked out for smoking spice.