Is only part of the building permit enforceable? How long is the building permit valid?

Wow! Thank you very much for the answers!

Regarding the validity of the building permit, see the state building code RLP § 74:
(1) The building permit and the partial building permit expire if construction work has not begun within four years of their delivery or if construction has been interrupted for four years. Construction of a project is only considered to have begun or not been interrupted if substantial construction work has been carried out within the period.

So start building the house immediately: build the entire basement and the granny flat. Once that is finished, I have about four years to continue. If it doesn’t work out within the four years, you can either apply for a change (e.g., no "rest" of the house at all or a smaller version). The risk would then only be a slightly oversized heating system, electricity and sewage (if at all), and the architect’s fees. That would still be okay in proportion (depending on what the architect wants).
From your experience, would a bank go along with something like this, say they provide 300,000 EUR and then want to see the entire house finished as soon as possible and the loan drawn, not just 150,000 EUR (you have to pay commitment interest anyway)?

Can the granny flat be completely separated from the house?

I don’t know if it counts as separated from a building law perspective, but this is the idea: The granny flat is two stories (plus basement part), next to it slightly offset is the front door, which will be built over in the remaining construction. So, the granny flat won’t be touched in the rest of the construction. Does that make a difference?

How about having the entire shell constructed as a “shell house” and then only finishing the granny flat?

The alternative is worth considering. Apart from the fact that you immediately have higher costs (shell + roof ideally in solid construction), I can imagine the psychological aspect is significant. If you live right next door and stare at the shell forever that you cannot finish, that can either be discouraging or prompt you to take on unreasonable financing.

The reason I considered this arrangement so carefully is the concern that if you first build only the granny flat as a house (small basement, 80 sqm house), you might not get approval for the rest of the construction in a few years.

Shouldn't the granny flat be inside the house? With a finished shell, you have the basic structure ready and psychologically you can convince yourself that people used to let the house dry for a few years anyway. I also think it won't cost much more than if, for example, you have to waterproof your basement without the house. Or later have to start building “from scratch.”

It will be difficult with the insulation or the heated envelope.

If it doesn't work out within the four years, one can either apply for a change (e.g. no "remaining" house at all or a smaller version). The risk would then only be a somewhat oversized heating system,

With a shared heating system, the project could suffer economically as a result. You will not need a change just to continue leaving the orphaned semi-detached house standing alone. But concerning the ghost cellar, I do not rule out a demolition order; one sometimes can hardly believe the conditions in Rheinlandpfalzistan.

The reason I considered the construct this way is the concern that if you first only build the granny flat as a house (small cellar, 80 sqm house), you might not get approval for the remaining construction in a few years.

What makes you fear that your building window could shrink due to an interim change in the development plan? – this would incidentally affect further construction on a then isolated cellar in the same way.

A friend of mine once had a nice multi-story apartment this way – the landlord did the opposite: he first moved into the granny flat but immediately completed the whole house (except for the cladding) and paid it off faster by renting out the larger part of the house; later he moved into the big part and did the finish.

I consider your thinking naive: apparently, you assume that making it a bit watertight is enough, and the cellar will stay fresh like frozen. Still putting the cellar ready for plastering without the house above will cost more than the interest for completing even the large residential unit in the first construction phase. Even for utility cellars, vacancy does not do a building any good.

In Greece, residential space is built like this ... however, that is because construction is only done with existing money, and therefore this staggering results.

How will you handle the money/financing? That’s not even a matter of wishing for something...

Shouldn't the granny flat be INSIDE the house?

Yes, yes! Viewed from the street: on the right the two-story granny flat, next to it on the left a small entrance area with front door and apartment doors, and then directly the large house (either directly ATTACHED to the front door canopy or ABOVE it).

It will be difficult with the insulation or heated envelope.

Basement?

With a shared heating system, the project could suffer economically. You will not need a change just to leave the orphaned semi-detached half standing alone any longer. But regarding the ghost basement, I do not rule out a demolition order; you wouldn’t always believe the conditions in Rheinlandpfalzistan.

What makes you fear that your building envelope could shrink in the event of an interim zoning plan change? – that would affect continuing construction on a basement then left isolated in the same way.

A friend of mine once had a nice multi-story apartment this way – the landlord did it the other way around: he first moved into the granny flat but immediately finished the whole house (except for the cladding) and paid off faster through renting the bigger part; later he moved into the large part and completed the finish.

I consider your thinking naive: apparently you imagine that making it a bit watertight is enough, and the basement will stay fresh as if frozen. Putting up the basement ready for use without the house above will cost more than the interest for completing the larger residential unit in the first construction phase. Even for utility basements, vacancy does no good to a building.

For temporary sealing of the basement, I was thinking of bitumen sheets, like with a flat roof. The basement can already be used (stairs and access are from inside) as an office etc., and would thus also be heated and ventilated.

Maybe the worry that the second phase will not be approved is unfounded. If you do it this way (first approval, then a second), you would somehow have to reopen the existing basement of the granny flat, or the exterior wall becomes an interior wall and a doorway breakthrough would be made.