Here we can see list of some Well-known ports and Registered ports in TCP/UDP, When we look at the port number 2086 it is assigned for two different services, one is official for GNUnet and other is unofficial for WHM.
Exactly this port number duplication cause any issues when we install both services having same port number in our server?
What does it mean, these same port number is assigned, one for official and other for unofficial purpose ?
You have to distinguish between port numbers registered by IANA (Internet Assigned Number Authority) and commonly used port numbers. Port 2086 is only registered for GNUNet (see https://www.iana.org/assignments/service-names-port-numbers/service-names-port-numbers.txt), but is commonly used also for WebHostManager.
In practice you could use any ports you like inside an application, i.e. it is not forbidden to use registered ports for other purposes or use unregistered ports. But it might cause conflicts with other software using the same ports, so it is better to respect registered ports and register your own ports if your application is of some importance.
Apart from that, more and more applications just move to a protocol on top of HTTP, because this is the only port open on most firewalls :(