Hi @,
So here is an update after having installed Bitmessage in a fresh Debian 9 on a VM as suggested by 0brand.
Verdict : Connection was working 
So I went back to my Whonix Workstation and used the version I found and downloaded here : https://github.com/Bitmessage/PyBitmessage/releases
And guess what ? I am glad to inform you that connection also works on Whonix 
Just use the latest release 0.6.3.2
This is the same version I used on my Debian connected on freenet.
The problem was from my point of view that I was using a beta version 0.6.3.2-0bc1df and I was not aware about that…
Hope it helps 
What about you guys who encountered some problems with your connection ?