On a MAAS cluster, if I do a "juju bootstrap", it creates a bootstrapping node from one of the free machines in the MAAS cluster, which becomes machine 0.
Is it possible for me to make the MAAS server itself the bootstrapping node?
I'm going to assume you mean the maas-master, the provisioner, in which case no; not at this time. In order to deploy something with MAAS and Juju the machine needs to be enlisted within MAAS otherwise Juju has no idea where it is or how to talk to it. If you were to enlist the maas-master then when you did "bootstrap" it Juju and MAAS would end up wiping and re-provisioning it. In doing so you would lose the maas-master.
Containerization and other co-location features are landing soon (including new provider types) which will allow you to pack more density in to a single machine. So in theory, you can soon run a bootstrap then deploy services on to the bootstrap, shrinking the number of physical machines needed in a deployment.