In various embodiments, a subsequence-based encoding application generates subsequences based on a source sequence associated with a media title. The subsequence-based encoding application then encodes both a first subsequence and a second subsequence across each of multiple configured encoders and at least one rate control value to generate, respectively, a first set of encoded subsequences and a second set of encoded subsequences. Notably, each configured encoder is associated with a combination of an encoder and a configuration, and at least two configured encoders are different from one another. Subsequently, the subsequence-based encoding application generates encoded media sequences based on the first set of encoded subsequences and the second set of encoded subsequences. Finally, the application selects a first encoded media sequence from the encoded media sequences based on a first target value for a media metric to subsequently stream to a first endpoint device during playback of the media title.