The physical remote (A1294) needs to be linked to the box, before it will execute its commands. Do both steps, first the unlinking, then the linking again. If your Apple TV remote isn’t working - Apple Support - Internet Archive (second half of the page).
The software remote on iPhone requires that the network settings on Apple TV have been configured first, as it only works for devices on the same home network. It also needs a [different] functional remote to enter the connection code on the Apple TV (3rd generation) [A1427 or A1469]. Also see: discussions.apple.com/thread/254506732.
As hcsitas pointed out, you will not get much use out of it, compared to a few years back (some services no longer support this model), or compared to more modern generations (much more and much better functions).