IMHO this is not an SOP fist fight.
Delete them as you please, just don't bust the level off.
IMHO it is more an airmanship and awareness tool issue. At times like this I always ask a relevant question, depending on the issue. In this case the FMC has a hard altitude in its data base for the SID. ATC clear you for the SID. You enter the altitude in MCP. Now, for the briefing you have a displayed confirmation between the FMC and MCP about the clearance. To delete the altitude in the FMC requires extra steps, effort, crew confirmation, (I'm sure you wouldn't do it on your own, would you).
The question is; how have you improved the situation by deleting the FMC Altitude? You haven't; but you've spent conscious effort & thought doing it. Why? There are some operators that depart in VNAV, or will use that mode after flaps up. VNAV will capture the FMC ALT. By removing it you are relying solely on MCP. We do so many things with belt & braces. Removes the braces, and if the belt is too lose, your trousers fall down.
I flew with a couple of operators who did have an SOP. If the SID cap was not associated with a WPT then it was not in the FMC data base. It was a requirement to enter the cap at a suitable WPT in the FMC, for the reasons stated above. IMHO seemed like a good idea.