If both transistors are powered/biased simultaneously, then the pop should be minimal since there is no "powering up" time. You may need to tweak the biasing. Switching between transistors IMO is for auditioning parts unless the resulting sounds are very different. That's the breadboarder in me talking.
Off the top of my head I think the Muffin Factory switches between transistors as a feature, but I wouldn't switch between them mid song for example. While the Muffin Factory is a cool concept as a pedal it tends to be option overload with all the dip switches. I pick a setting I like then forget it with the exception of the knobs.