I suppose that this just supports the concept that we all have our own personal needs, desires, and aesthetic tastes. For me, I'd much rather deal with the side opening saddlebags, and keep the carried weight down low, than pull the saddlebags off and run with just the top case on. The only reason I can envision that being "the best way to go" is the commuters in CA that need to stay thin to lane split. To me, having the side bags off and a rear trunk sticking up in the back just looks odd. But as I said... to each his own.
On solo day rides I generally leave the left bag empty and put any gear I need in the right side bag, because it will be facing up when the bike is parked on the side stand. The empty left side bag is where I can quickly stuff my helmet and gloves at stops. I do use those nylon buckled straps inside to help arrange and restrain the gear from shifting around inside the right bag.
My rear trunk only goes on if there will be a passenger (her back-rest) or for an extended trip, which usually includes said passenger.
For my first EOM trip I went without the pillion, but with the rear trunk for the added storage space. I had not yet mastered the concept of minimalist packing when riding, back then. Now I would easily fit my own gear into the two side cases. The trunk without passenger did create some squirrelly aerodynamics, but only at higher speeds and in the turbulent air of interstate highways with the truck traffic. Below ~75 mph it has never been apparent to me under any conditions. It isn't an unsafe condition, as far as I can tell, just an undesirable wobbly feeling.
My aesthetic preference (and yeah, I even like the black Bagster tank cover). On tour, in Nova Scotia, June 2011
