Tip: Layer 3 backgrounds and tides disappear when you hit a message box, so plan your level around that. For example, you can add a sublevel without layer 3 at the start/midpoint, and include your message there.
Works fine for the most part. I only have disabled the "don't disable clipping..."-thing for the shellless Koopa which had the glitch that the Koopa behaved weirdly (also affecting the alternating height jumping Para-Koopa).
The Koopa also behaves like a normal shell when eaten by Yoshi so keep that in mind when creating levels with it.
The Koopas also are invinsible to fireballs but not to capes. You can fix that if you do the hex edit mention in the ROM Map for $02A0B9.