Well the true purpose of the "linked/unlinked" function in the envelope window is to allow a modulation envelope to have either the same loop length as the notes clip (linked) or have a totally independent loop (unlinked). A note clip can have associated linked and unlinked envelopes.
A by-product of "linked" is that it visually shows note positions in the background of an envelope window. This allows you to easily apply modulation with regard to note position. Also, the envelope has a visual time signature grid, which will be the same as the note clip, and using "draw mode" it is easy to apply quantised modulation.
You can draw a modulation envelope any way you want to match with note positions (e.g. start fractionally later than the note or change value over the duration of a note). However, if you subsequently change note positions the envelope will not be changed to match the new note positions.