Hi Mariano,
this is a common question for external projects integrated inside the Pharo image. And we have an issue with version numbers, but let's try to keep that separate.
Fixes to the code of external projects integrated inside Pharo should be done upstream (on the external project itself), not in the Pharo image. This is what is currently happening with the GT tools, NeoJSON, Zinc, and probably a few more. So, as a maintainer of such a projects in github, say, you can ask people to create issues on your project, pull requests and the like, and this is the only way bugs found in Pharo in your release project should be corrected. Then, everytime a new version of the Pharo image is built, a version of your project is integrated; and you can add an issue to update your project to a newer version inside Pharo.
(Was I clear with that description? Feel free to ask or correct me :))
Now, about the package versions. There is an issue with metadata-less mode and a few quirks about the way Metacello check versions to upgrade packages, and the issue is open. Two ways forward are possible: David Allouche pointed one by saying ordering between versions (without checking the numbers) can be resolved by checking if one is an ancestor of the other... and the other is that, with Skip work on the github api, it becomes possible(*) to retrieve the version info from github without git and avoid those -Cypress.1.
Thierry
* There is a bit of code to write, of course, but most of it is reusing what already exists inside Skip github and GitFileTree.