My chapters have always run naturally about 3.5-4,000 words each. I don't purposefully hold them to that standard it just seems to happen that way. . . . I'm using scene breaks to split it up
If I understand this correctly, you use traditional chapter breaks to split up the first 60K words, inserting them where the scenes end.
Then for 13K words, you
don't put chapter breaks at the end of scenes.
Then you start using chapter breaks again.
Because of this, you end up with a humungous-long sixteenth chapter.
Yes. I think this would feel a little odd to the reader.
It wouldn't be, strictly speaking,the length of the humungo chapter that would puzzle the reader. She'd just want to know why you suddenly stopped chaptering.
this is a story within the story it would feel weird to go: chapter 1-15 MC story, chapter 16, 17, 18, & 19 Antagonist story, and then the rest back again.
I've read lots of books that shift from one POV to the other, or one 'story' to another, or one time frame to another, without giving up chaptering.
That is to say, IMO, there's no reason a 'story within a story' should be only one chapter long.
If you want to set off the 'story within a story' in some way that goes beyond simply letting the reader know that time and place have shifted, perhaps you could insert an introductory page before and after the 'inner story'.
The 'introductory page' could just say -- 'Twenty Years Before,' or 'Paris, The Secret Dungeon in the Rue Rivoli,' or 'Clive Dennison,' or whatever would signal the reader this was a new 'story'.