EDIT:
For anyone who sees this later-on, I solved this problem by quickly realising that it would be really helpful to run ScrollTrigger based animations in parallel all the time, therefore it made sense that GSAP would implement it by default. I realised that that was what was happening.
To solve this, I created the second timeline inside the onComplete callback of the first ScrollTrigger based timeline, and therefore the second timeline only gets added to the master timeline whenever the first timeline finishes completely.
