Once you reach the boss area, you may be disappointed (though not particularly surprised) that the boss doesn't show up regardless of character, as it does in Sonic 3 & Knuckles. In fact, there are no objects placed in the boss area at all.
As it turns out however, Knuckles' boss is actually present within the game's code in a half-finished state. The following PAR codes will add the boss to Marble Garden Zone 2's object layout at its usual coordinates from Sonic 3 & Knuckles, overwriting the last starpost in Sonic and Tails' route:
063822:3E78 063824:0000 063826:B100
The screen lock can be modified using the code 04A490:3D78, but since the object has several hardcoded coordinates in its movement routines, it will quickly jump outside the screen and never return. This is fixed with the following codes:
04A572:3E18 04A578:FFA8 04B0C6:0038 04B0CE:3E18 04B176:00F8
For convenience's sake, we can push up the bottom screen boundary by setting the Camera_target_max_Y_pos RAM variable to $28, which is achieved with the following codes:
As we can see, the behavior of the object is very similar to that of the final version, except for being displayed in front of the level blocks, and not producing any debris when passing through them. And although the player can damage it, the boss doesn't have a death handler, so it can't actually be defeated.