I don't understand why you need different boots for snow shoeing. I have one pair of winter hiking boots. They are not higher than just above my ankle, but they are waterproof/Gore Tex. I have gaiters for snow shoeing, that go up to mid calf. I wear them (the shoes) whether it's -10 or 35 F. Above that, I'm not usually doing snow sports. The difference is in the type of socks I wear, and the addition of chemical warmers.
And yes, I often bring several layers/choices for x country ski/snow shoe trips where there may be big changes in weather temperatures. Although mostly, it's either very frigid or too warm to ski/snow shoe, with melting snow!