How to plumb aquaponics systems that are far apart?

If you are eliminating "hole through the side simple overflow" then you have probably arrived at two pumps, with the return pump in a standpipe/sump which has a simple overflow into it to the maintain the level in the plant side, and is operated by a float switch on the sump/standpipe. Managing the return with a siphon is even more likely to cause a flood than drilling holes in the tanks.

I'd drill the hole for the overflow, and then use rigid pipe of generous size (since you only have 2" of head you need a large pipe) for the return attached to it, as I consider the hole with a pipe near the top of the tank far less risk than one pump failing and the other pump merrily overflowing. Or some cockamamie siphon setup failing and the pump merrily overflowing.

You could have a second float switch that disables the fish-side pump if the plant side sump gets too full.

Augmented siphon: one pump and a perforated pipe.

For this scheme you need a serious pump and a perforated pipe on the plant side.

Your pump pulls water from the fish tank into the plant tank. The water is pushed into a PVC pipe along the side of the plant tank near the top. The PVC pipe is perforated such that some of the pressurized water leaves the pipe. Some water from the plant tank enters the pipe. I considered also using a drip hose for this but I think the inside of the drip hose would eventually get clogged with particulate waste from the fish side.

Water entering the pump side of the pipe will be under a lot of pressure and much will escape thru the holes of the pipe.

Farther down the pipe the perforations end. There is a second smaller pipe joining the formerly perforated pipe at a steep angle. The idea is that flow in the large pipe produces a Bernoulli effect and low pressure where the pipes join, causing water to flow in from the plant tank.

At the end of the large pipe is a hose leading back to the fish tank. Pressure in the perforated pipe is lower now but still higher than the outside water, and so enough to push water up and over the top. Once it has made that little climb the water will go downhill back to the fish tank.

This has one pump which is nice. Some water from the fish tank will make it thru the perforated pipe and be returned to the fish tank which is not a tragedy. If the pump stops, nothing will flood. If the water level rises in the plant tank there will be more pressure assisting the siphon effect on the return circuit.

Obviously with too many perforations all the pressure will be lost in transit of the pipe and there will not be enough left to get over the top. Too few and you will just be circulating water from and back to the fish tank.

I have this idea that more is better: as pump strength increases you will push more water out the perforations and also have enough residual rapid flow to maximize the Bernoulli effect and intake thru the angled intake pipe.

Ultimately the outflow thru the perforations needs to match inflow via Bernoulli effect. This is the point where the architect hands the plans over to the engineer.

If height "C" of the lower point of the outlet is between "A" and "B" the siphon should stay full of water.

This corresponds to your third drawing.

It could be handy to add a valve to be able to direct the flow from the pump into this pipe in reverse to prime it (ie, fill it with water and push the air away). This will probably work best if the pipe diameter is small enough to get a fast enough flow that carries away the air.

It may be simpler to just make a hole in the side of the tank on the left and connect the pipe there, which would get rid of the siphon, but it could also leak.