It's entirely possible that home owners are NIMBYing this due to perceived impacts on their house values.
But I'm not sure you're right about developers wanting to just develop a few luxury condos and artificially restrict the number of units they build. It seems like that would only work if there was a near monopoly on who was allowed / able to build in SF.
They make money on building units; not building units is not really benefitting them.
Per the article, the per-unit costs of all the planning / permitting / construction / land / special interest earmarks make the per-door cost to be the $1 million quoted. That already puts that into "luxury condo" price range. It might be that the ROI might be better for the developers if they decide to spend an extra $100k on premium tile so it really is "luxury". It might be that selling them as non-luxury really isn't profitable. After all, if as a customer you're going to need to spend at least $1.05 million on the unit (break even for developer + 5%), wouldn't you rather get a $1.25 million luxury apartment for not that much more? (1mill + 100k tile + 14% profit). For the developer in my made up scenario, they're making 3x the profit, while you're "only" spending 20% more on the more desirable luxury version.
I'm sure if the permitting process were quicker / easier, the barrier to entry for developers of all sizes would be lower. The per-door cost would be lower, and you wouldn't need a massive war chest of cash to ride the 3-year permit process. This would also make the economics on non-luxury units make sense.