Batman Doom with some fixes making it nice to play in Crispy Doom sourceport,
taking advantage of its 'limit-removing Vanilla' approach providing support for Batman Doom's massive DeHackEd patch.
Batman Doom by ACE Team Software fixed for Crispy Doom (limit-removing Vanilla, non-Boom, non-ZDoom sourceport), with episode selection lumps removed (Crispy has a feature to display episode selection lumps if provided by a PWAD), Vanilla Doom DeHackEd fix not required anymore and some typos in the DeHackEd text fixed (e.g. Azrael's Gloves and Blastgun having swapped names, 'Major Kroll' instead of 'Mayor').
Crispy Doom is better for playing Batman Doom than Vanilla/Chocolate as it has options for uncapped framerate with or without VSync and provides the optional crosshair, mouselook and direct aiming functionality which is useful for non-centered and non-hitscan weapons like batarangs and smoke bombs.
It keeps telling me in ZDL that "flats not found in IWAD file."
Are you trying to run this WAD in Crispy Doom with ZDL? ZDL is for ZDoom family ports only that Crispy doesn't belong to.