With my PNP Link ECU, I use the external Knock Link unit with the factory knock sensors. Without the external knock unit I think you can just log knock (don't quote me), but not use it to limit the engine which mine can do.
I have fuel pressure limiting the engine. It uses a digital fuel pressure signal and a spare ECU map to limit the engine, if fuel pressure drops too low. I have staged fuel pumps as well with second one kicking in at 15 psi boost.
You could also do the same with oil pressure as well.
If you swap to a 2 wire ISCV, you can free up at least 2 inputs (outputs?) as the mkiv ISCV uses 4 wires.
There is no traction control with the Link PNP, you would need the Fury or Thunder (better option as has high speed sensors that can be used with ABS without needing a signal divider).
The Link PNP does not have VE tuning, but that is available on some later model Link ECU's. e.g. G4+, Fury, Thunder