Good-day @Anonymous , glad to have someone who feels the same. After @RichardHammerl's advice on the workarounds, I spent some more time on this today. The following are my conclusions:
1- I was feeling too lazy to create a package from scratch so I downloaded a library with appropriate 3D package for my resistors and capacitors. Replaced the components with the new ones and then pushed it to Fusion360 and viola, there was my component with 3D package in 3D PCB workspace. Although this method works for generic components, not all components come with a 3D package. For example I had found a sweet 3D model for a barrel connector and used the "Add Custom 3D package" to add it to my PCB component via package editor. That 3D package failed to sync in Fusion 360 and the sweet 3D barrel design never appeared. My conclusion is the "Add Custom 3D package" does not work as intended.
2- This time I opened the schematic and board directly in Fusion360>New Electronics Design, uploaded the schematic, linked the board and validated design consistency for schematic and board. After that I did the same thing that I did with eagle, replaced the old components (without 3D package) with new components (with 3D package). Then viewed it in 3D PCB and there were my new components with 3D package. There were still a lot of components without 3D package available so I tried the Open Device>Create New Package>3D package generator. There was no option to upload custom step file like that in Eagle's Package Generator. The templates of Fusion's 3D package generator were that of generic components and not of the one that I wanted (DC barrel connector in my case). To conclude, these are lots of steps to replace a 3D package but the purpose (replacing with a custom step file) is not served in my case.
I have arrived to the above conclusions by figuring the workarounds as mentioned by @RichardHammerl, please correct me if I am wrong anywhere. It is evident that the older version which had PCB workspace was more straightforward and practical. I have still not figured out how to add a custom 3D component step file without making it from scratch. If anyone is able to accomplish that please add to this post.