That will depend on what type of inputs/outputs these extra PI/PO are.
Are these scanin/scanout? Have you used scan constraints?
Do you really need to compare them?
Why do you want to reduce extra and unreachable DFFs? Since they do not contribute to design functionality, its better leave them unmapped and not to compare them.
There is no scanin and scanout pins. I have already used the scan constraints.
How to decide whether we need to compare them or not ?
Actually these are in large numbers like:
-Out of 166 PI's only 35 are mapped and 131 are Extra.
-Out of 358 PO's only 20 are mapped and 338 are Extra.
Doesn't such large number in EXTRA contribute to something? Or we can just ignore them.
As you have applied scan constraints and scan ports are not present in design Synthesis tool has added those PI scan Input and PO scan ouputs.
You can ignore them