Both modes will be similar when only two pumps are used. These differences between these options are more apparent when 3 or more pumps are involved. If you need the two pumps to alternate with each other, it would be better to use the Permanent opposite mode.

The stress put on the pumps is not so much on the wave pattern (sinus or right-angled). What matters more is how quickly you set these to move between the min and max percentages. If you're ramping up and down in 1 seconds between 10% and 100%...that will put more stress on the pump than 10% and 100% in 5 seconds.