As each part has it’s own efficiency loss (or non-ideal power conversion) that likely means in the end less juice got into the battery. A regular stepdown/up regulator doesn’t care about the panel voltage and current on it’s input. It only cares if itself is outputting 5 volt. That means the solar panel is probably operating at less efficient power point, meaning you’ll get less watts out of it. And the battery charger is another additional source of loss. The MPPT tries to draw just enough current out of the panel such that the panel voltage doesn’t go to either extreme (up or down) and that means the power coming out is optimum. Check the Sunny Buddy hookup guide to see what it this power-point is all about.
Measure the current and voltage coming out of each stage (solar panel, step-up/down regulator, battery charger). You’ll need multiple multimeters (stages x 2) for that to get some hard data on what you are loosing. And I DO mean you should measure both voltage AND current to get power. Only voltage doesn’t say anything.