At 125% some resources might not have space left to be placed due to earlier placed bonuses taking all the spots; for all resources to be placed in the ratios defined in xml one should pick 75 or 50%.
100% should be fine too though, especially on larger map sizes.
But yeah, we might want to increase the relative amount of certain strategic resources; but best of all would be to add more events that add resources like that on the map after map generation when certain conditions are met, e.g. no player having resource but have tech to use it (increased chance to trigger event the more players that meet the condition).
Mines, and other improvements, does spawn resources, and resources that are rare on the map has greater chance to be spawned by an improvement than a resource that is bountiful on the map, so having resources on 50% at map-gen will increase the amount of improvements that can discover resources and might make iron/copper and so on more frequent in the long run.