The short answer is no, but what you really need to know is why, so let's discuss the longer answer instead.
This is in fact how many rebellions operated in the past, and unless you have a massive groundswell of popular support, it doesn't work because tying yourself to a base means you need something that your established government is better at controlling;
Logistical support.
Once you're dealing with bases and territories, you need to be able to safely move food, supplies, equipment, troops, engineers, et al through that territory. Also, you're now in a position where whatever happens, you need to defend that main base. That means that your guerrillas always have to come back for defensive duties, regardless of their missions, whenever that base is found and attacked. You're also exposing yourself to the application of siege tactics, which brings up the other point; you need a steady and reliable source of food and water for the people in this base. That's much harder to hide in terms of unaccounted supplies than is a distributed network of operatives.
There's a very good reason why modern 'revolutionary' and/or terrorist outfits work in the cells model; it means that if the authorities break into one cell they only get a small part of your network, and the others have time to adapt to that cell missing from their midst. Also, the supplies of food, water and equipment don't raise too many suspicions when procured in many small domestic purchases from many geographic locations. That also makes logistics easier because each cell operates independently, buying from local markets meaning that there IS no supply line to defend, or keep secret, let alone a whole base.
Militaries on the other hand need supply lines still for reasons other than what the original theories discussed; modern militaries are not supporting massive movements of personnel, they're supporting massive movements of equipment. Keeping (say) a squadron of F-18s combat ready and running daily sorties in a modern conflict takes parts, people, fuel, munitions, etc. and it's the support of these massive machines that the cell model can't handle. Also, modern armies need their chains of command so that their attacks are coordinated with deep precision in order to achieve a very specific objective, which is something that the cell model also doesn't support.
Your rebels on the other hand have a rather unfocused objective; overthrow the government. To do that, you don't need coordination on the scale of a modern military, and you don't need big machines of war. You only need teams out there wreaking chaos wherever and however they can.
It's a lot easier to break a machine than it is to keep it running smoothly, whether that machine is a computer or a nation. Even in medieval times, this was true.
The biggest issue you're going to have with the times and a cell model is that cells rely more heavily than other military models on communications, especially covert communications. This isn't practicable in a medieval environment, at least not in the manner that one would expect. Still, if you have a good team of hither-to unknown agents crossing the countryside as travelling salesmen (or similar) who are also great at secreting messages into their loads, saddlebags, etc. then it's entirely possible that such a model could be achieved. The one advantage that you have is that your shapeshifters all have a common enemy that they see as an existential threat, so you don't have to keep them on point in terms of the cause; you only need to keep them on point as to how to prosecute that cause. That, at the very least, should make things easier.
Once you've wreaked enough chaos with Guerrilla warfare, then you have to start organising on a larger scale and bases become necessary. But in the early stages where the rebellion is small and prosecuting a strategy of decentralised strife, having a base just provides the enemy with an easy target should it ever be revealed.
