A common solution is

“write it for standard tuning since that is the way, it is actually played on the guitar, and make a tuning note on the manuscript”

However, it might be a good idea to ask the guitarist who is going to play the music.

Unfortunately, the best answer is It depends.

Fortunately, this is a very old road. During the Ukulele Craze of the '20s and '30s, there was no standard pitch for the instrument—the 1st string would be tuned anywhere from A–D with the gut strings in use at the time. Much popular sheet music would print the piano part in concert pitch and the ukulele chords in B (the most common tuning for the soprano back then) with a note at the beginning of the piece (or each song) indicating the correct tuning.

Solve the problem for the expected player. I would notate in standard pitch with a note that the tuning is to be changed.

As a bassist, I often encountered pieces in Solo Tuning which is a whole step up (again, gut strings). The accompaniment is in the correct key with the solo part provided in both tunings. Nowadays, soloists will have instruments in both tunings as metal strings designed for one tuning don't work well tuned up or down. The soloist tuning transposes.

It's hard not to agree with you sir. It really depends on what you are transcribing.