Not sure if this is new since I have little experience with the game prior to 1.1 but playing as Moltar I have Terran Colonization but colonizing a terrain planet still uses up Resilient Settlers causing my Colony Base in another system to get auto-cancelled. Naturally the expectation is that RS wouldn't trigger if you have the right colonization tech.
Thanks for your feedback. Resilient Settlers offers two benefits: a) allows you to colonize a world even if you don't have the colonization tech; and b) removes the morale penalty on the newly founded world for 15 turns. Now, since Terran is not "Ideal" to you, since you're playing with the Moltar, you will incur morale penalties if you don't use resilient settlers. So, the design decision in this case was to apply RS in all colonization efforts on non-Ideal worlds as soon as the ability is ready.