Tziera is right in most situations. WD specific example - Soul Harvest gains the effect of all runes. The damage of it will be determined by the rune you select to cast. If you pick Languish, it's cold damage.
Another situation would be using Wormwood, which cast Locust Swarm at enemies for free. This is a runeless Locust Swarm unless you have a specific rune on your bar - then it takes that damage type (Searing Locusts makes it fire damage, etc).
Non-WD exception is the Wizard's Archon form - the damage type isn't determined by the rune, but rather by the largest bonus elemental damage % - if you have 20% fire damage, it's fire. If you have 20% cold and 19% fire, it's cold, etc.
TL;DR - The F&R act as a multiplier to your other damage types. If you are losing 9 discipline, let's say you go from 109 to 100 discipline (with no other multipliers). In scenario one (SoJ) you have 109x40% added damage or 4360% damage. In 2, (F&R with 100 discipline) you have 4000% damage, but it is multiplied by Focus buff so 1.5x4000% - 6000% and then buffed by Restraint so 1.5x6000% = 9000%.
Clearly F&R provide significantly more damage, and it is because of how damage is calculated.
0
Tziera is right in most situations. WD specific example - Soul Harvest gains the effect of all runes. The damage of it will be determined by the rune you select to cast. If you pick Languish, it's cold damage.
Another situation would be using Wormwood, which cast Locust Swarm at enemies for free. This is a runeless Locust Swarm unless you have a specific rune on your bar - then it takes that damage type (Searing Locusts makes it fire damage, etc).
Non-WD exception is the Wizard's Archon form - the damage type isn't determined by the rune, but rather by the largest bonus elemental damage % - if you have 20% fire damage, it's fire. If you have 20% cold and 19% fire, it's cold, etc.
Not sure offhand if there are other exceptions.
*Edit* Fixed mistake.
3
Here is an explanation of what you are asking (not by me, just linking): https://us.battle.net/forums/en/d3/topic/18710646678
TL;DR - The F&R act as a multiplier to your other damage types. If you are losing 9 discipline, let's say you go from 109 to 100 discipline (with no other multipliers). In scenario one (SoJ) you have 109x40% added damage or 4360% damage. In 2, (F&R with 100 discipline) you have 4000% damage, but it is multiplied by Focus buff so 1.5x4000% - 6000% and then buffed by Restraint so 1.5x6000% = 9000%.
Clearly F&R provide significantly more damage, and it is because of how damage is calculated.