I travel often between the Bay Area and San Diego and almost always have at least two bikes with me: a road or gravel bike, and an enduro MTB.
First, invest in some wheel bags if you haven't already — the padded ones are best, and make sure you buy the appropriate size for the wheel you have, e.g., a 29" wheel with a 2.5 will require a slightly higher volume bag.
With the front wheels off and the bikes placed in opposing direction it fits no problem with a 54cm road bike and a Large Evil Following. I'm just unloading from a trip so it's a little messy, but here's an image for reference: