We have a documentation page that outlines our stance on this, which is inline with the way pinyin transcription is done in all Chinese->English dictionaries.
The pronunciation of the pinyin is different from its transcription for tone sandhi in most cases, as you point out. For example, if you look up 不用 in nearly any Chinese->English, the headword pronunciation will be “bu4yong4”. Likewise, in any sentences that also have pinyin, it will be transcribed as “bu4yong4”.
However, for the audio generated, we have a list of exceptions for these cases to ensure that it is generated in a way that reflects its actual pronunciation. E.g., for “bu4yong4” the audio that plays is indeed “bu2yong4”.
I think there are things we can add here to reduce confusion for those new to this concept:
- Block e.g., “bu2yong4” as an accepted answer with a pop-up that indicates one should not correct for tone sandhi when in the transcription.
- Accept the tone sandhi as an answer with a note.
I think we have an item for the first one, which I can see ourselves doing at some point for special cases like 不 and 一.
(edit: here is another thread of a user encountering the same issue: (Feature Request) "Phonetic" tones as alternatives to "written" tones)