> Having a one-to-one romanization for each Hiragana phonetic is far more logical for learners

It depends on the learner’s (and textbook author’s) goals. Sometimes, having a phonetic transcription of the more common pronunciation is a more important consideration.

Historically, Hepburn’s transcription pre-dates Japanese orthographic reform. He was writing “kyō” back when it was spelled けふ. Having one-to-one correspondence to kana was not a goal.

So writing sensē is kinda on-brand (even if Hepburn didn’t write like this, because in his times it still wasn’t pronounced with long e).