OK, this is interesting.
When I put the following in /services/runtime.cfg:
org.openhab.links:autoLinks=true
I can see changes in the following file:
trs80@odroidxu4:/var/lib/openhab2/config/org/openhab$ cat links.config
:org.apache.felix.configadmin.revision:=L"2"
autoLinks="true"
service.pid="org.openhab.links"
… but NOT in PaperUI! In there I still get “Item Linking / Simple Mode” set to “OFF” even after refreshing the page, and “Items” is still visible in Menu -> Configuration…
However, if I comment that out, and instead put the following in /services/runtime.cfg:
org.eclipse.smarthome.links:autoLinks=false
… then I get the changes in PaperUI, but NOT in the aforementioned file…
Anyway I think this is just an interesting side note. Insofar as my problem in OP, I am a bit embarrassed to say I think it has actually been working fine the whole time(?), and perhaps I was just mistaken due to (I don’t know what?). Because I think the only changes are (as I mentioned above):
- “Items” present in Menu - Configuration, and…
- “Item Linking / Simple Mode” toggle set to OFF in PaperUi
And I already have that. In fact, I think I had it all along… 
So, sorry for the confusion…