What do you mean, exactly, with "runway frequencies" ? ILS ? Key West doesn't have any.
COM frequencies ? We haven't change or override any of the COM frequencies from the default scenery, since the flag in the scenery to override COM frequencies is not set
I believe FSD's KORD for FS2020 has the same issue.
No, KORD is not the same because, opposite to KEYW, it DOES exclude the default frequencies and it provides them with its own so, from the "how the scenery is made", in relationship to COM frequencies, they are completely different.
Also, is not clear if your problem happens only with the Cessna Longitude, or with others.