BBA Deli Rye bread -- overproofed? Under-kneaded?

Greetings, able bakers!

I was making my first attempt of the "Deli Rye" (part wheat, part rye flour) in BBA a couple of days ago. While I'm extremely satisfied with the flavor, I didn't get as much of a rise in the proofing as I thought I might. My first attempt was with free-standing batards, which ended up rather flat. A couple of days later, I decided to employ a loaf pan (8.5x4.5in), but even then, the top of the proofed loaf didn't quite peek over the top. There were some marks at the top where it looks like the edge of the dough may have "broken open".

I used KA bread flour and Anson Mills rye flour, along with a recently refreshed (one day prior) wild yeast starter and SAF red for the commercial yeast. I machine-kneaded it on medium-low for about five minutes total. The dough just  barely  passed the windowpane test, but I was also afraid of over-kneading and ending up with a gummy dough, as the book warns against. I let the loaves proof at 90 minutes, covered, at room temperature (72F). Any advice from folks that are familiar with this bread or have run into similar issues before?

Thank you, and happy baking!

--Byron