I don't know if official Rocksmith charts always make such a distinction between two repeat chords when there's a short rest between them. As an author you have the option to explicitly use the "sustain" status on a chord to make the chart display tails for the notes in the chord and it will be obvious how long each chord in a handshape is to be played. If you want a separate handshape it's as easy as putting the crazy status on that next chord, or manually marking handshape sections. As far as i know Ubi notetrackers dont author rests, if i remember correctly they argued that it could clutter the screen and that the guitarrist would know after a few plays when to rest by themselfs. I dont agree with it, i always put a crazy when a rest is needed and when there is a sustain on a chord that i want to highlight i use as you said a sustain status on it. about sustain cuts in EOF, i always cut sustain from chords and notes. Its usually 1/16 or 1/12 that i cut but it varies depending on the BPM of the song and the distance of the notes to each other. I feel that the result is always clearner and looks that way more professional. Slides, bends and other special cases are a different story. You just need as a notetracker enough experience to know when to use what.