I've had this talk/discussion MANY MANY times before

"(FileSize - Downloaded Size) / Total file download speed" is a very *basic* view on more complex topic.
Internally there are many different calculations done.
One of it is the (Rest Size/Speed) calculation that you have in mind, but also it is important to take
the slowest download (longest eta) into consideration.
Easy example: two situations
2 Files (50MB and 150MB) loading at 1MB/s each file
-> Your calculation would return 100 secs ETA...
-> JD calculation returns 150 secs ETA
Now download A finished while B is still running, there are two possible outcomes
1.) B will continue to load at 1MB/s
-> Your calculation was wrong and the ETA will increase
-> JD calculation was correct and just counting down
2.) B will speed up to 2MB/s
-> Your calculation was correct and the ETA just counting down
-> JD calculation will adapt and the ETA will decrease and faster counting down
Your *easy* calculation with (Rest/Speed) does ONLY provide good ETA in case the assumption that you will always max out your download speed but that isn't the case in real world and heavily depends on many many factors like connection/ISP/free/premium.....
(rest/speed) may result on wrong ETA in meaning of that it may take longer than expected
JDownloader ETA calculation might also be wrong but instead of taking longer to finish, it may only result in faster download.
So JD returns the *best guess* at maximum ETA while (Rest/Speed) always returns the *earliest finish time*
I don't say that the current calculation is perfect but myself and many others prefer an ETA that is realistic than an ETA that increases over time.
I better know that it might 10 mins and it can be finished after 5, than waiting 5 mins and then realising it takes/took 10 mins in the end.