Of course they don't. But if even a small percentage of their userbase uses this on even a small percentage of their photos, that amounts to a massive amount of storage. It doesn't cost Google very much to store all those images, but those users will have to pay for more storage. Even thought it isn't significant to Google when a single person does it, it becomes highly significant when millions of people do it.

A million people adding 12MB each would be 12TB in increased storage sales. Is that really significant in increased profit if you set it off against the cost of providing the storage, the computational cost of generating 12TB of images, plus the salaries of the developers to write and then maintain this feature?

I think it's more likely that they're doing it because they think it makes their product better, increasing sales that way instead.

This line of reasoning doesn’t make sense because 3MB is marginal for the amount of work put in to develop this feature.

Google photos offers a save as copy / save as original feature when editing photos and videos. Removing the save as original button would be cheaper and significantly more effective.