What could cause a toilet to bubble occasionally, even if sewer line is clear?
Regardless of how clear the drain lines are, if you have blocked, obstructed or inappropriately sized plumbing vent stacks, the bubbles could be emanating because the air being displaced as the drain line fills from the shower, have no easier path of resistance than your toilet.

TL:DR You've cleaned and investigated downstream, maybe it's time to look upstream.