If you TWYS then you will put spaces between the components and these will no longer indicate only a line feed. (see my examples).
ISTM that the most important thing is that cloud codes entered via the drop-down list are clearly distinguishable from the ones transcribed directly. That way, the science team will always know which cases they need to treat differently. So the precise details of the format used when directly transcribing the cloud codes should not matter too
Currently, the pre-defined items in the drop-down list only contain a fixed range of alphabetic characters, plus one hyphen. So any transcription format that includes at least one character not
in that set (such as a space, dot, ampersand, etc) should be enough to distinguish it from a pre-defined cloud code.
The real issue is that most users encountering this for the first time:
might naturally assume that the writer meant Cumulonimbus and wrongly select Cum-Nim from the drop-down list. So some prominent warnings regarding multiple cloud codes could be very helpful.