Honest question: Why would you want ligatures in plaintext? Especially in code, wouldn't that be weird as some people tend to manually align their code? Like,
modular_raft = 10
spam = 20
The "ft" in modular_raft should convert to a ligature so (I assume) it will then take one character, instead of two. Then developers viewing that source would have different alignments, depending on whether they use Sublime 3 or not.
(EDIT: Formatting.)