My wife is writing a book, and just got a draft back from an editor.
The editor noted extra commas in numerous sentences like this:
He looked at her closely, but all she said was, "I am truly glad we will be living in a nice, safe fort, and not one of these wild frontier towns."
The extra comma in question is after fort.
The argument was that the comma was not needed because it was separating dependent clauses. My wife put the comma there to create a verbal pause.
There were other places for which similar commas were not within character quotes (a character wasn't speaking). This may be a different animal:
Dani had begged for a day to rest some, and to catch up on the numerous small duties she'd not been able to see to during the past week.
She's gone through all of the grammar and style guides she has access to, and hasn't found whether it's permissible or not. I'd guess at least that it should be done consistently one way or the other, but don't know which way.
Best Answer
It looks to me like you've already answered your own question. "It should be done consistently." Follow one consistent pattern within the narrative. If you (by which I mean your wife) want(s) to insert extra commas in the dialog to show pauses, that's your prerogative, but make sure that there's actually a reason for the pause caused by each additional comma. If it doesn't give any additional meaning, remove it.
The prescriptivistic and potentially outdated grammar of Elements of Style lists a rule (in Chapter 1, part 4) for placing a comma "before a conjunction introducing a co-ordinate clause" (unless the conjunction is and or but and both clauses have the same subject). That could work as a reasonable ground rule for where to insert commas in the narrative, but it can be customized as you see fit. It's a novel, not a piece of academic writing, so it's up to you to decide on your own rules for when commas are needed.
There are plenty of acclaimed modern authors who use almost no commas at all. The general modern approach to commas is the fewer the better. If you can't think of a specific reason why a sentence needs to have a comma, it's better to leave it off.