The Deoxys Camouflage Clause was added to Gen 3 Ubers as the resolution to this thread. Functionally, Deoxys will behave identically to how you remember it before. Like suggestion 3 of Inspirited's OP recommends, it's basically a "do-nothing" clause that is there for clarity.
Additionally, Gen 3 Anything Goes matches now more strictly enforce the "1 Deoxys forme per cartridge" limitation, by simply limiting the player to only bringing one forme of Deoxys. You can bring multiple of the same forme, but only one forme is allowed per team, as it is impossible to obtain multiple Deoxys formes across different games without ROM hacks. The Deoxys Camouflage Clause, which again doesn't enforce anything by itself, is independent of this validation.
Additionally, Gen 3 Anything Goes matches now more strictly enforce the "1 Deoxys forme per cartridge" limitation, by simply limiting the player to only bringing one forme of Deoxys. You can bring multiple of the same forme, but only one forme is allowed per team, as it is impossible to obtain multiple Deoxys formes across different games without ROM hacks. The Deoxys Camouflage Clause, which again doesn't enforce anything by itself, is independent of this validation.