Again from a diagnostic and user friendliness point of view...

Firstly, it would be nice that full pedal travel did in fact yield a blade that is open against it's fully open stops.

I'd then set this as 95% in the Sensor linearisation in the software. ( it should never go higher...if you display higher, then you know there's a fault )

The closed...some EFI setups will run a fully closed blade and all idle air functions will be from the idle valve or motor etc.
Some will prefer the blade to be partially open, with the idle valve doing less work.

Aftermarket..up to you really and how good the system is. I prefer a good warm idle with the idle valve almost closed and using a small fixed blade opening. Idle valve has less work to do, and it's usually easier to achieve a good strong idle
Whether you set this base to 0%, or the fully closed to 0%..up to you. I'd be happy to have this base "closed" position displayed value at 5%.

Again it means you can monitor position and if it changes for some reason ( it often does slightly from cold-warm ). Or you may not use an idle air valve at all.
But having a closed value of say 5% allows you to adjust idle, overrun settings etc without having to manually reset the blade/software to 0% each time