Something to consider, though it pertains to the old WEG system.

In that system, the Mon Cal suffered a penalty to skill checks tied to specific Attributes when in arid environments... but they also enjoyed a bonus to skill checks tied to those same specific Attributes when they were in moist/damp environments.

If it was a little humid outside, the D6 versions of the Mon Cal got a bonus die on certain skill checks. So there could very easily be a lot of instances where Mon Cal PCs would be enjoying a free bonus die that applied to a number of useful skills. Every so often, a GM might set an adventure in an arid environment, and the Mon Cal PC would suffer a one die penalty to counteract the bonus die that they'd frequently been enjoying.

The FFG version doesn't have any of that. The Amphibious species ability doesn't provide any bonus dice even under the circumstances it applies to. So in that light, why should a penalty be applied to a species ability that's not likely to come up very often?

Well, in long arm of the hutt for edge of the empire there was a section where a certain player species had more setback dice, and one had none.

So applying setback or boost dice based on a species' traits, as long as it isn't malicious and unfair or singling out one player