Ideally Bazel would have native support for this, see bazelbuild/bazel#13048.

Until then one can work around this by detecting a tool configuration as motivated in bazelbuild/bazel#14444 (comment) using the approach described in the Bazel code base here in the settings rule and switch between separate mode and exec_mode flags.

However, such a workaround breaks config_settings such as defined here. As they cannot determine whether we're in a target or exec configuration and cannot switch to the appropriate flag accordingly. One workaround to that would be to split the config_settings into target_debug and exec_debug, etc. However, this means that downstream users would have to know which setting to switch on, which doesn't work for targets used in both an exec and a target configuration.

Until a concrete need arises, it's best to wait for Bazel to have builtin support for this feature.