Deed registration only works at builder that let you build farmer buildings, i. e. buildings that require a farmer to activate. Flats are not farmer buildings (but residences) so you can't apply deed registration when building farms.
good point. I'd missed it was just farmer buildings.
In all other cases it does not really matter in which order you build the farms and farmer buildings. The only requirement is you build at least one farmer building.
So if you've already upgraded all your farms to estates, you can go to the estate action and pay for a farm and upgrade it to an estate in a single action?