I never acquainted with types.nix, is there some fundamental reason that either of two freeform submodules couldn't work when left and right have disjoint explicit options?

with import <nixpkgs/lib>;

evalModules {
  modules = [
    {
      options.foo = mkOption {
        type =
          types.either
            (types.submodule {
              freeformType = types.attrsOf types.str;
              options.marker_a = mkOption {
                type = types.str;
              };
            })
            (
              types.submodule {
                freeformType = types.attrsOf types.str;
                options.marker_b = mkOption {
                  type = types.str;
                };
              }
            );
      };
      config.foo = {
        marker_b = "bar";
      };
    }
  ];
}

{ foo = { marker_a = «error: The option `foo.marker_a' was accessed but has no value defined. Try setting 
the option.»; marker_b = "bar"; }; }

I believe the issue is the left and right type's check function.

either will use whichever type fist passes check value, and iirc submodules just use something like check = isAttrs

nix-repl> with lib.types; (listOf int).check [ true false "hello" ]
true

nix-repl> with lib.types; (addCheck (listOf int) (builtins.all builtins.isInt)).check [ true false "hello" ]
false

The other issue with marker options (marker_a, marker_b) is how should definitions be merged that don't include the marker? E.g.

foo = lib.mkMerge [
  { something_freeform = "hi"; }
  { marker_a = "there"; }
]

You don't know which marker is defined until all merging is done.

In a simple case like this, you could refactor this as one submodule with both markers, and then add some extra logic/conditions within the submodule and/or in the optinon's final apply function.