The CR2032 is usually only used in applications that draw very little current and, as such, run for 'years' without interruption. Under which circumstance I can't see why you need to make an extra effort for what would (normally) be an isolated occasion.
Equally, the application of the CR2032 won't include charging facilities which will necessitate purchasing a separate charger for the Lithium version.
Whether or not the difference between 3V and 3.6V is significant will depend on the application - some circuits that require 3V will have a supply tolerance of 10% so 3.3V is the limit..... you'll have to specify what the use is before we can confirm with any accuracy.