Thank you so much for your interesting, thorough and detailed observations. First of all, let me start with the last section of your resumé. I completely agree with you in your approach-to-transcriptions to lower the interval in some cases and then to transpose it up with another different interval. From my own experience it not only works for the lute, as you mentioned, but also for keyboard transcriptions.
About your first observations (the use of rests in a few bars), I am sure you're right on some details but less sure on others. However I feel it's important to realize that transcribing a tablature-notation, with limited information about duration of notes (especially related to middle voices) always will imply a certain amount of personal interpretation based on what you think is the best way to express the spirit and dynamics of the music.
The middle section is the most interesting part. Here I am confused. We know that in the 16th century in Italy the standard practices related to music notation, pitch level, tuning and selection of keys were rather different from present-day practices. My starting point of the Fantasy XIV is the tablature notation of Molinaro (1599). Six courses with some specification where to put your left hand fingers. No information about the tuning, key or pitch. So how to translate the tablature into standard notation for the 20th century classical guitar (tuned in E)? It is not to difficult to recognize in the tablature the characteristics of f# - minor as the 'concealed-key'. How it sounded for Molinaro we do not know. Probably not as f# - minor. Probably much higher.
My conclusion is that we both like to play the Fantasy in E-minor, but what we hear will be different, caused by not-using a capo or by putting a capo in II or III position. In my transcription I have suggested to put the capo on III. I play E -minor but I hear G - minor. and that might be the key Molinaro had in mind if he lived in 2019.