We are using versions/releases for releases and milestones. It would be good to be able to check a box on the release to distinguish it from milestones. It is useful to have both releases and milestones in the same place, as they are often very closely related.

I don't see why there can't be both.

And yet...here we are: 

JSWCLOUD-20254 Milestones - Create and track feature requests for Atlassian products.

JSWCLOUD-17652 Milestones for Basic Roadmaps - Create and track feature requests for Atlassian products.

Versions and releases are confusing for most of my customers; I tell them they just need to understand that Version and Releases labels are used interchangeably within JIRA. This is non-desirable. Either allow us to rename the constructs or keep the naming 'Versions' as it exists within JIRA proper.

In our company we use release and milestone as two separate entities. Release is used for software releases and milestone for high level planning. A milestone may include multiple releases. Showing milestone on the Gantt chart would be cool feature as well.

Agreed, we just used the release for a grant-funded project and use the Project Phases as releases for one project and the high level project objectives as releases for the other project, which is confusing our non-techy users