That's because you are using a guitar, which is not perfectly in tune no matter how you tune it.

For an equal temperament instrument (like a midi keyboard), transcription would be seamless.

For a fretless instrument, transcription can be made seamless, if the player is good at intonation.

However, the timbre of the instrument can still be a little different for each key (e.g. open strings vs fingered notes), but that's a nuance on instrument rather than transcription per se.