This might be interesting to you: GPIO binding: Switch to pi4j · Issue #4976 · openhab/openhab1-addons · GitHub
Glad to hear that. Both should behave the same.
That’s by design. One of the biggest misconceptions with openHAB 2. Have a look here: Recommended way to backup/restore OH2 configurations and things? - #44 by ThomDietrich - You can use config files or PaperUI or whatever else might be available to configure the internal database. These methods can also be mixed. openHAB will never change your config files. That’s a feature 
Regarding your log, I’d be interested in the readings in the last few lines. I suspect they are continued like that on a regular basis? Something seems to be wrong with the way the script is working or executed by openhab (despite your previous findings…).
My advice: Move the execution (temporarily) into a rule. A rule gives you more flexibility and the full result of your execution. This way you can see what’s actually going on. Check the rule here: Speedtest-cli Internet Up-/Downlink Measurement Integration → var String result = executeCommandLine("your command", 120*1000)