Acoustic instruments certainly have a timbral difference between notes. More importantly, I think, is the sonorous range of an instrument. In particular if an instrument runs to C vs F# you may or may not have access to a full octave in a certain register. This tritone difference can have a significant timbral impact on certain instruments, especially when played near the pitch range of an instrument. In those situations the choice of key has a notable impact, meaning scales where your top octave ends at a higher pitch have a brighter sound vs darker otherwise.
As for a more complex emotional relationship between certain root pitches I suspect this isn’t absolute or universal. Having said that, despite most people not perceiving absolute pitch, I think there is something of a recognition perceived in commonly heard keys on common instruments (such as the piano) perceived by virtue of the timbral changes I mentioned. In this regard I think there is a weak, but perhaps measurable, difference in experience of songs performed in different root pitch (vs just digital transposition of the audio where the timbre may remain). Perhaps even a slight familiarity or unfamiliarity: my take though, is that any such effect is weak.
More importantly to me, is that on some instruments (notably the piano) it requires quite different hand positions to play notes of the same function in different keys. As such, when composing by playing on an instrument, the mechanical differences yield different musical choices. The result, I suspect, is differently melodic choices being made. For a guitar I guess chromatic transposition for melodic parts is simple, but often chords get played in different positions so perhaps guitar based music tends toward differing chord choices. In any case I suspect there will be some bias towards certain melodic or harmonic structures on certain instruments in certain keys.
When composing on paper or on a piano roll I don’t think this applies to the same extent. Perhaps compositions on a staff still suffer from some form of “note choice bias” by the placement of the lines (and necessity for ledger lines beyond the core range). Perhaps, therefore, piano roll composition is the most “egalitarian” method. One method I sometimes use is to choose a key for a song (at random, but with the mode based on the feel I want) then play different parts in different keys, and chromatically transpose the midi into the key of the song. My perception is that this results in different musical choices than I might otherwise have made.
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