Mesa (Bryce) doesn't use some settings from custom World

I lowered the sea level (29) and Depth Base Size (3) and set biome to Mesa. I also raised biomeScaleWeight.
World generates mostly like expected but is seems like Mesa (Bryce) is not using the lowered baseSize in some parts.

The stone on the screenshot is going up to the normal sea level.

How to reproduce

1. Create new custom world using the seed 1104859589434701128 and this preset:

   {"coordinateScale":684.412,"heightScale":684.412,"lowerLimitScale":512.0,"upperLimitScale":512.0,"depthNoiseScaleX":200.0,"depthNoiseScaleZ":200.0,"depthNoiseScaleExponent":0.5,"mainNoiseScaleX":80.0,"mainNoiseScaleY":160.0,"mainNoiseScaleZ":80.0,"baseSize":3.0,"stretchY":12.0,"biomeDepthWeight":1.0,"biomeDepthOffset":0.0,"biomeScaleWeight":2.0704226,"biomeScaleOffset":0.0,"seaLevel":29,"useCaves":false,"useDungeons":false,"dungeonChance":8,"useStrongholds":false,"useVillages":false,"useMineShafts":false,"useTemples":false,"useMonuments":false,"useRavines":true,"useWaterLakes":false,"waterLakeChance":4,"useLavaLakes":true,"lavaLakeChance":80,"useLavaOceans":true,"fixedBiome":33,"biomeSize":4,"riverSize":4,"dirtSize":1,"dirtCount":0,"dirtMinHeight":0,"dirtMaxHeight":256,"gravelSize":33,"gravelCount":0,"gravelMinHeight":0,"gravelMaxHeight":256,"graniteSize":33,"graniteCount":20,"graniteMinHeight":0,"graniteMaxHeight":30,"dioriteSize":33,"dioriteCount":0,"dioriteMinHeight":0,"dioriteMaxHeight":80,"andesiteSize":33,"andesiteCount":0,"andesiteMinHeight":0,"andesiteMaxHeight":80,"coalSize":17,"coalCount":0,"coalMinHeight":0,"coalMaxHeight":128,"ironSize":9,"ironCount":0,"ironMinHeight":0,"ironMaxHeight":64,"goldSize":9,"goldCount":0,"goldMinHeight":0,"goldMaxHeight":32,"redstoneSize":8,"redstoneCount":0,"redstoneMinHeight":0,"redstoneMaxHeight":16,"diamondSize":8,"diamondCount":0,"diamondMinHeight":0,"diamondMaxHeight":16,"lapisSize":7,"lapisCount":0,"lapisCenterHeight":16,"lapisSpread":16}
   

2. Make sure to have biome fixed to Mesa or Mesa Plateau (it seems like there is another bug while using presets)
3. /tp -1650 100 -1950