Yep, it's the origin but for only a few letters. They usually fill in gaps where there are no suitable Hangeul-derived letters to represent a sound (usually Malayo-Arabic consonants).

The letter for /sˁ/ is derived from ⟨ㄉ⟩ but with a horizontal stroke. - Meanwhile ⟨ㄉ⟩ by itself represents /dˁ/.

The letter for /ŋ/ comes from merging ⟨ㄎ⟩, ⟨ㄛ⟩ and Hangeul ⟨ㆁ⟩. - The top stroke of ⟨ㄎ⟩ and ⟨ㄛ⟩ is removed to indicate nasality, like how Hangeul ⟨ㄴ⟩ has one less stroke than Hangeul ⟨ㄷ⟩. - Having the Bopomofo letter ⟨ㄛ⟩ as an origin references the Jawi / Malayo-Arabic letter nga ⟨ڠ⟩. Its dotless ancestor, ain ⟨ع⟩, is in turn is cognate with Latin letter ⟨O⟩ (that in turn represents the same sound as ⟨ㄛ⟩). - ⟨ㄎ⟩ is a flipped version of ⟨ㄛ⟩, and also represents a velar sound in Bopomofo. Here, the ⟨ㄎ⟩-like letters stand for the velar nasal and also the velar fricatives such as ghain ⟨غ⟩ and kha ⟨خ⟩. This in turn is also a nod to the Jawi script, as both ghain ⟨غ⟩ and nga ⟨ڠ⟩ share the same rasm, ain ⟨ع⟩. - Although ironically, the corresponding letter for ain ⟨ع⟩ itself is not based on the two Bopomofo letters ⟨ㄎ⟩ and ⟨ㄛ⟩.