I think it helps to understand that the engine has two completely independent EGR systems. Both of them are controlled by an electric motor working the EGR valves themselves, and these default to "closed", so once a tune is applied, these will never open again, and neither one is likely to become an issue by itself. They're just a component that is simply along for the ride.
The regular, or "high pressure" as we now call it, EGR system is simple: it is a pipe attached to the exhaust manifold portion of the turbocharger, at right angles near the #4 cyl exhaust port, that runs around the head above the bellhouse area, and goes to its valve that is sandwiched between the intake throttle flap and the intake manifold itself. You needn't physically do anything to these pieces.
The "low pressure" EGR system takes its exhaust post-DPF, through the little filter pipe off a little bung on the downpipe, and first goes into the EGR cooler and valve assembly that is bolted to the back of the block, and from there, has a little stack that goes up into the turbo inlet adapter flange bolted to the turbo itself. All that gets done there is the filter pipe gets removed (the delete pipe will have no bung to attach it) and the little two-bolt flange where it bolted to the cooler/valve assembly gets the little block off plate affixed. That's pretty much it.
You don't need anything else. No "race pipe" or nonsense like that. If it really bothers you that much that the high pressure pipe is present, you can certain dig it out (it's not quick, stuff in the way, and the studs on the turbo can break off and then you're really screwed). To do that, you'd need another block off plate at the exhaust manifold. You would also want one at the EGR just because over time the valve itself even though it is closed it can weep a bit of oil that is being carried through the breather system (which is a normal thing, that's how it works). By leaving that pipe in place, however, any oil weeping past the valve will just harmlessly push into that pipe, and drain back down into the exhaust every time you shut the engine off.
When you delete, you'll also not need the EGR pressure sensor (the one on the valve cover the ECU uses to monitor the low pressure EGR flow) or the DPF pressure sensor (over my the aux. fuel pump, the one the ECU uses to monitor DPF load). You also won't use the lower temp sensor that plugs in down under the car, along with the exhaust throttle and lambda sensor, nor either of the two EGT sensors that go into the top of the OC/DPF assembly.... you WILL need to put the upper lambda sensor back in (some early pipes also provided a spot for the upper ... orange connector... EGT sensor, so if the pipe has that, that's what goes in there).
People really overthink this stuff.
