The minimum lot size element of zoning relates to the creation of new parcels. Once the site itself "exists" it is usually the maximum density that acts to limit the development potential of the site. I haven't seen it all by any stretch of the imagination, but I don't recall seeing any municipal or county zoning ordinance in Calif that didn't function that way.
In most jurisdictions, an R3 (which is a medium density) zoning reg will have a maximum density somewhere in the 1000sf of lot area per unit range. For the sake of discussion and to make things simple lets assume that is the case here. If so, the maximum buildout for this site might by 6 units, subject to the provision of sufficient onsite parking and other development criteria.
So will as-if-vacant site value for a site that can be built out with 6 units be greater than an as-improved value for the existing residential use? If the subject is an SFR it's very common for such properties to be redeveloped into units, depending on the market conditions in effect for that location. But that's a question to be answered rather than an assumption to make.
If this subject is an SFR the only way you'll be able to figure out whether the SFR use if the as-is HBU is to compare the value as an SFR to the underlying site value. And the only way you're going to be able to do that is to identify and analyze other multi-family zoned site sales, preferably with the same R3 zoning.
The dominant unit of comparison for muilti-family land will be price/unit, particularly when your comps have various zoning designations and varying development potential.