How do I get rid of flooded caves in custom overworld dimensions?

This issue is caused by the 1.18 aquifers. Any noise cave between around 30 to 60 will be flooded. MCreator's base code for dimensions seems to have the aquifers set up to spread everywhere else as well.

You will have to lock the code, and then modify the dimension json file. The options for "fluid level floodness", "fluid level spread" and the lava/water barrier aquifers. Set the "from value" and the "to value" to larger numbers. This will "stretch" the noise generator, making the aquifers spaced farther apart. You can also play around with the noise cave settings to make them more sparse, and generate more noodle/spaghetti caves(similar to how caves used to be).

The options for "fluid level floodness", "fluid level spread" and the lava/water barrier aquifers. Set the "from value" and the "to value" to larger numbers.

Could you please elaborate a bit on what you mean by the "from value" and "to value"? Neither is present for me on any of the fluid options you listed. There are from and to values for the initial and final density, and xz/y scale parameters for the fluids, but after having messed with both nothing seems to have changed the constant "all caves flooded below Y=60" in my custom 1.20.1 dimension.

I fixed this by setting sea_level to -128 (my dimension goes to -128) But this will remove oceans, but that was not a problem for my dimension as it does not require oceans.