It's amazing how quickly you adapt to a method of entering notes into a sequencer. Back in the old Nokia flip phone days when you could program your own ringtones, I became a total whizz at entering the notes of any tune into the phone via the numeric keypad.
I had OctaMED in the early 90's. Absolutely loved it. No MIDI, no external gear, just an 8-bit sampling cartridge which I used to sample everything that was worth sampling from my CD collection. I would also sample single guitar notes and intervals up and down the neck at various pitches, and would combine them to make any chord I liked. Entering notes was basically entering numbers with the numeric keypad into a giant vertical list of numbers, and once I got going with that thing I could write any part that came into my head, even complex jazz-fusion lines. It doesn't matter how tedious or fiddly a workflow is, if you're motivated to reach an end result and you put the time in, it becomes second nature.
I can read and write music but these days I much prefer to write in the piano roll. It just makes more sense to me, and you can "see" familiar chord shapes in it just as you can see them on a stave.
Having said that, I think the guitar fretboard will always be the most familiar to me in terms of scales and harmony. I think in shapes! Even when I'm composing in the piano roll, I always keep the fretboard in my mind's eye.