It seems that when an agent has been added to one or more deploy environments then it is excluded from being used for build plans at all - even when capabilities dictate that it should be available.
You're right. If agent is dedicated to any deployment environment/project or build plan it will not be used for other jobs.
In Bamboo 5.13 we added ability to manage environment requirements so you don't have to use agent dedication for your deployments - https://confluence.atlassian.com/display/BAMBOO/Bamboo+5.13+Release+Notes
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