I could be totally wrong here but I think you get charged the extra PP if you have a fare break, I.e. if the two segments are priced as two different one-way fares (which you can sometimes get on a multi-city search) versus a “through fare” with a connection.

I recently had a flight from a city (let’s call it XXX) served by United Express to ORD to AMS with the XXX-ORD leg on an (economy-only) CRJ and the ORD-AMS upgraded with pluspoints.

When I called to move my XXX-ORD leg to another flight that had a first class cabin, I was told I would need to apply additional PlusPoints to get that segment in First (I class was actually available) because it was priced as two separate fares XXX-ORD and ORD-AMS.

I didn’t bother and the upgrade ended up clearing anyway.

Again that’s just one data point.