octave line pushes fermata up...

How can I avoid the fermata from being pushed away from its note when using an octava line on that same note?

I believe thus far there isn’t a global option to fix this. In Engrave mode you can drag the pause down (or set its Y start offset to a minus value) and if necessary you can drag the ottava line up (or set its Y offset to a positive value).

Same problem with commas, so it’s probably an issue with the octave line:
Screen Shot 2017-09-23 at 13.51.08.png

Octave lines are positioned along with slurs, tuplets, and articulations, and other items like holds/pauses, playing techniques etc. are positioned outside all four of those items. You will indeed need to move them in Engrave mode to change their relative order.

Seemingly related to this issue: fermatas appear inside lyrics that are positioned outside the staff. Since we can’t change lyric baselines yet, does this mean there is no way to make fermatas appear outside the line of lyrics?

No, you can go into Engrave mode, grab the fermata and nudge it up. The lyrics will stay put.

Daniel, excuse my ignorance but somehow that seems very strange… is this a rule referenced in some music notation book? (Sorry—I’m away from the office so I cannot check my references, but thought I’d ask just in case you remember.)

No, this isn’t a rule, but rather how Dorico works at present. Because of the complex nature of positioning these items, there are some compromises in Dorico’s behaviour at present: articulations, slurs, tuplets and octave lines are all positioned together, and at some point we will probably have to include both playing techniques and holds/pauses in this processor to fully resolve these issues, but that four-way processor is already the most complex of all of Dorico’s 100-plus layout processors, and re-engineering it to be able to handle two more types of items is not a small task. We can do it, certainly, but it needs time, and at the moment we have to remain focused on filling in bigger gaps in Dorico’s functionality.