Thanks so much for the great question! Honeycomb is indeed fatter than brood comb, and cross combing can be avoided by separating the top bars by about 1/8 inch once they start building pure honey comb. You can put in a spacing shim between the bars, or you can simply leave empty space for them to fill in with propolis.
Once the honeycomb starts being crossed, you can slice the comb where it is going askew and move it back in place on the starter top bar and secure it in place with a zip tie over the top of the bar. This will get a bit messy with the honey spilling out of the comb, but the bees will clean it up and reattach the wax in the correct place.
At this point in the season, I might not recommend repairing cross comb, since you don't want to divert their resources away from final preparations for the winter. You could wait to fix the comb until early spring and simply break off the crooked pieces leaving open spots for them to fill with fresh comb, while still maintaining most of the original structure.
I hope this helps!