It looks as though there is a way round BAM-3491 (Limit agents to given plans). For a deployment plan it is possible to select any agent irrespective of any constraints.
For example if a remote agent is dedicated to Project A and a deployment plan is created under Project B. For that deployment plan, clicking the Agents button under the other environment setting it is possible to select the agent dedicated to Project A.
We are running Bamboo Server 5.12.2.1 Build 51213