Now it's a matter of knowing if Tycho will upgrade to support more recent deploy plugin versions, and the requirements they impose on implementations of custom packaging types for modules.
Or the other way round. It needs to be investigated, but maybe it's more maven-deploy-plugin that needs to be made aware of non default packaging types coming from extensions.
At this point, it's not obvious which one is wrong; but since maven-deploy-plugin 2.x used to work with Tycho, the fact that it breaks with 3.x seems to be a regression.
If there are no such plans (or they'll take too long), it means I need to indeed hack some solution myself somehow.
If you have some resources to hack a solution, then instead of hacking something, please consider contributing the necessary patches to Tycho or Maven. Both projects are really welcoming contributions!
In the meantime, feel free to open a bug to Maven and/or Tycho about this issue and posting your analysis and experiments; this will help in identifying a proper solution.