So, if we disregard the possibility that some operators used this as MCP ALT during climb (which I highly doubt), there clearly were pressurization incidents when using the "reset FLT ALT" technique during step climbs, so Boeing decided to strongly recommend setting final cruise level on the pressurization panel.
They way they have written the explanatory background that you quoted indicates the opposite. They have specifically said that some operators are repeatedly resetting FLT ALT during CLIMB. Something which you highly doubt but it is annoying Boeing enough for them to issue an FCTM amendment.
They have not said that some operators are forgetting to reset FLT ALT during a step climb or step descent during CRUISE. Let me repeat that... They have not said there is any issue during cruise that they feel the need to address. If they had wanted you to set the "highest expected cruise altitude", don't you think they would have said that? I have not read the phrase "highest cruise altitude" in any Boeing document.
So, the important thing is not to confuse "intermediate altitudes during climb" with "step climbs during cruise". They are two different phases of flight.
The first is the CLIMB phase of flight. The second is the CRUISE phase of flight.
Boeing is clearly referring to the CLIMB phase of flight. That is why they use the phrase "during climb".
Intermediate level-off during CLIMB is handled with the MCP only. Step climbs and descents during CRUISE involve 3 settings: MCP, FMC and FLT ALT. I didn't make that up, it is SOP clearly published in the FCOM. If you can't find it, I'll give you the references.
Just set the FLT ALT to match the FMC CRZ ALT. Iif you subsequently change the FMC CRZ ALT, you change the FLT ALT. It's not complicated, and it's Boeing SOP.
If your operator publishes a different SOP then follow that. In that case the argument is with your operator not with you. But if your operator thinks they are following Boeing SOP, they may be mis-interpreting this FCTM amendment, and perhaps they should pick up the phone to Boeing and sort it out. Boeing will probably say "set final cruise alt", but get them to explain that. Final cruise alt is generally defined as TOC alt, not TOD alt (hence all this disagreement).