Make sure logical settings that the user might set for FATES used in logic are standardized

Logical variables used for namelist defaults rely on them being set to ".true." rather than the valid options for the string.

@ekluzek is the way that I'm passing the value of `use_fates_lupft` here an ok way to make sure the nocomp default is appropriately set? I know this way works as it passes unit tests, but it's different from the way `use_fates_sp` is passed in (i.e. by being added to the `nl_flags` list and referenced that way), so I wanted to double check.

_Originally posted by @glemieux in https://github.com/ESCOMP/CTSM/pull/2507#discussion_r1672752527_